I've checked it in ToT Chromium and the updated password is saved as expected. 

battre@ Could you please attach chrome://password-manager-internals log? On which OS it's reproducible?

One caveat, in order to see an updated password in chrome://settings/passwords, the password needs to be hidden and then shown again, for some reasons it's not updated when visible.

====== 1) Go to https://rsolomakhin.github.io/autofill/ ======

Message: PasswordAutofillAgent::DidStartProvisionalLoad 
The new state of the UI: 0
Message: PasswordAutofillAgent::SendPasswordForms 
only_visible: false
Security origin: https://rsolomakhin.github.io/ 
Number of all forms: 7
Form is a password form: {
Action : https://example.com/ ,
New password element : ,
Origin : https://rsolomakhin.github.io/ ,
PSL match : false,
Password element : password ,
Password generated : false,
Scheme : HTML ,
Signon realm : https://rsolomakhin.github.io/ ,
Times used : 0,
Username element : name 
}
Message: PasswordManager::CreatePendingLoginManagers 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Number of pending login managers (before): 0
Adding manager for form: {
Signature of form: 11161482137509878464
Signon realm: https://rsolomakhin.github.io/
Origin: https://rsolomakhin.github.io/
Action: https://example.com/
Form name: np
Form fields: 
name: 3489289364, type=text
password: 2051817934, type=password
}
Message: FormFetcherImpl::Fetch 
FormFetcherImpl::state_: 1
Number of pending login managers (after): 1
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Generation possible account creation forms: 1
Message: Generation: no non-blacklisted confirmation 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Server predictions: {
Signature of form: 10519201316547307791
Origin: https://rsolomakhin.github.io/
Action: https://example.com/
Form fields: 
name: 3489289364, type=text, SERVER_PREDICTION: NAME_FULL
address: 509334676, type=text, SERVER_PREDICTION: ADDRESS_HOME_STREET_ADDRESS
city: 2098554694, type=text, SERVER_PREDICTION: ADDRESS_HOME_CITY
state: 1878375253, type=select-one, SERVER_PREDICTION: ADDRESS_HOME_STATE
zip: 569224803, type=text, SERVER_PREDICTION: ADDRESS_HOME_ZIP
country: 3654076265, type=text, SERVER_PREDICTION: ADDRESS_HOME_COUNTRY
email: 420638584, type=text, SERVER_PREDICTION: EMAIL_ADDRESS
phone: 1635119699, type=text, SERVER_PREDICTION: PHONE_HOME_CITY_AND_NUMBER
}
Server predictions: {
Signature of form: 9118006264864951514
Origin: https://rsolomakhin.github.io/
Action: https://example.com/
Form fields: 
name: 3489289364, type=text, SERVER_PREDICTION: CREDIT_CARD_NAME_FULL
CCNo: 2038457965, type=text, SERVER_PREDICTION: CREDIT_CARD_NUMBER
CCExpiresMonth: 1874155745, type=select-one, SERVER_PREDICTION: CREDIT_CARD_EXP_MONTH
CCExpiresYear: 2992415869, type=select-one, SERVER_PREDICTION: CREDIT_CARD_EXP_4_DIGIT_YEAR
cvc: 2836487997, type=text, SERVER_PREDICTION: CREDIT_CARD_VERIFICATION_CODE
}
Server predictions: {
Signature of form: 2414262792596421371
Origin: https://rsolomakhin.github.io/
Action: https://example.com/
Form fields: 
name: 3489289364, type=text, autocomplete=off, SERVER_PREDICTION: NAME_FULL
address: 509334676, type=text, autocomplete=off, SERVER_PREDICTION: ADDRESS_HOME_STREET_ADDRESS
city: 2098554694, type=text, autocomplete=off, SERVER_PREDICTION: ADDRESS_HOME_CITY
state: 1878375253, type=select-one, autocomplete=off, SERVER_PREDICTION: ADDRESS_HOME_STATE
zip: 569224803, type=text, autocomplete=off, SERVER_PREDICTION: ADDRESS_HOME_ZIP
email: 420638584, type=text, autocomplete=off, SERVER_PREDICTION: EMAIL_ADDRESS
phone: 1635119699, type=text, autocomplete=off, SERVER_PREDICTION: PHONE_HOME_CITY_AND_NUMBER
}
Server predictions: {
Signature of form: 13447302746672280161
Origin: https://rsolomakhin.github.io/
Action: https://example.com/
Form fields: 
name: 3489289364, type=text, SERVER_PREDICTION: NAME_FULL
address: 509334676, type=text, SERVER_PREDICTION: ADDRESS_HOME_STREET_ADDRESS
city: 2098554694, type=text, SERVER_PREDICTION: ADDRESS_HOME_CITY
state: 1878375253, type=select-one, SERVER_PREDICTION: ADDRESS_HOME_STATE
zip: 569224803, type=text, SERVER_PREDICTION: ADDRESS_HOME_ZIP
country: 3654076265, type=text, SERVER_PREDICTION: ADDRESS_HOME_COUNTRY
email: 420638584, type=text, SERVER_PREDICTION: EMAIL_ADDRESS
same: 2770979949, type=checkbox
s_name: 2114321042, type=text, SERVER_PREDICTION: NAME_FULL
s_address: 1183287088, type=text, SERVER_PREDICTION: ADDRESS_HOME_STREET_ADDRESS
s_city: 427350874, type=text, SERVER_PREDICTION: ADDRESS_HOME_CITY
s_state: 2524899095, type=select-one, SERVER_PREDICTION: ADDRESS_HOME_STATE
s_zip: 152203277, type=text, SERVER_PREDICTION: ADDRESS_HOME_ZIP
s_country: 3978392364, type=text, SERVER_PREDICTION: ADDRESS_HOME_COUNTRY
s_email: 2115670289, type=text, SERVER_PREDICTION: EMAIL_ADDRESS
}
Message: PasswordAutofillAgent::SendPasswordForms 
only_visible: true
Security origin: https://rsolomakhin.github.io/ 
Number of all forms: 7
Form found on page: {
Action : https://example.com/ ,
Form name or ID : addr1_1 
}
Form is visible: true
Form found on page: {
Action : ,
Form name or ID : form300 
}
Form is visible: true
Form found on page: {
Action : ,
Form name or ID : form300off 
}
Form is visible: true
Form found on page: {
Action : https://example.com/ ,
Form name or ID : cc1_1 
}
Form is visible: true
Form found on page: {
Action : https://example.com/ ,
Form name or ID : np 
}
Form is visible: true
Form is a password form: {
Action : https://example.com/ ,
New password element : ,
Origin : https://rsolomakhin.github.io/ ,
PSL match : false,
Password element : password ,
Password generated : false,
Scheme : HTML ,
Signon realm : https://rsolomakhin.github.io/ ,
Times used : 0,
Username element : name 
}
Form found on page: {
Action : https://example.com/ ,
Form name or ID : addr1_1off 
}
Form is visible: true
Form found on page: {
Action : https://example.com/ ,
Form name or ID : addr1_sections 
}
Form is visible: true
Some control elements not associated to a form element are visible: false
Message: PasswordManager::CreatePendingLoginManagers 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Number of pending login managers (before): 1
Number of pending login managers (after): 1
Message: PasswordManager::OnPasswordFormsRendered 
Message: PasswordManager::CanProvisionalManagerSave 
Message: No provisional save manager 
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Message: Generation invalid PasswordForm 
Generation possible account creation forms: 2
Message: Generation: no non-blacklisted confirmation 
Message: Generation: no non-blacklisted confirmation 
Message: FormFetcherImpl::OnGetPasswordStoreResults 
Number of results from the password store: 0
Message: PasswordFormManager::ProcessMatches 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: Generation: no server signal 
Message: Generation: no server signal 

====== 2) In the Name/Password section generate a password. ======

Captured password manager logs are listed below. Logs are cleared and no longer captured when all password-manager-internals pages are closed.
Message: Show generation popup triggered manually 
Message: Generated password accepted 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: PasswordFormManager::ProcessMatches 
The new state of the UI: 2

====== 3) Verify that the password appears in chrome://settings/passwords ======

[no output]

====== 4) Append any character to the password ======
[I focussed the password field, appended the character 'a' and unfocussed the password field]

SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: PasswordFormManager::ProcessMatches 
The new state of the UI: 2
Message: FormFetcherImpl::Fetch 
FormFetcherImpl::state_: 1
Message: FormFetcherImpl::OnGetPasswordStoreResults 
Number of results from the password store: 1
Message: PasswordFormManager::ProcessMatches 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: PasswordManager::Autofill 
wait_for_username: false
Message: Generation: account creation form already found 
Message: PasswordAutofillAgent::OnFillPasswordForm 
ambiguous_or_empty_names: false
Number of potential forms to fill: 1
form_data's wait_for_username: false
form_contains_fillable_username_field: false
username_field_name empty: true
password_field_name empty: false
Message: FillUserNameAndPassword in PasswordAutofillAgent 
Message: Username to fill matches that on the page 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: PasswordFormManager::ProcessMatches 
The new state of the UI: 3
Filled password element named: password 
Message: FormFetcherImpl::Fetch 
FormFetcherImpl::state_: 1
Message: FormFetcherImpl::OnGetPasswordStoreResults 
Number of results from the password store: 0
Message: PasswordFormManager::ProcessMatches 
SSL errors present: false
IsPasswordManagementEnabledForCurrentPage: true
Message: Generation: account creation form already found 

====== 5) Observe that no credential is stored ======

- At this point chrome://settings/passwords has no entry for https://rsolomakhin.github.io/ (even if I refresh the page)
- At this point, https://rsolomakhin.github.io/autofill/ still shows the key icon in the omnibar. If I refresh, the key icon is gone.

Chromium	69.0.3470.0 (Developer Build) custom (64-bit)
Revision	abd8e1e73eafee7c8d16e47a830733af2fcad8bc-refs/heads/master@{#569613}
OS	Linux

The reason is the following:
1.When password is updated PasswordFormManager makes presaving, which consists of removing previous password and adding new one.
2.UI code in ManagePasswordsState::ProcessLoginsChanged processes passwords updates, finds that there is deletion and initiates filling in PasswordFormManager by calling PasswordManager::UpdateFormManagers();
3.PasswordFormManager fills the generated password and not it's not considered generated anymore (because it's filled).
4.As result PasswordFormManager::PasswordNoLongerGenerated is called, which removes the generated password from the store.

The immediate reason of this regression is the CL https://chromium-review.googlesource.com/c/chromium/src/+/1092745 which captures username. But this CL is correct (before this CL, no username was captures and UI code can't find deletion, because it matches by username). 

The main problem is that UI tries to propagate information about deletion to backend, despite this deletion has nothing to do with UI. I'm going to fix it. 

Also it would be better not to autofill generated password to avoid such regression in future.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/cdc4b34576d0d2a5b9391b5dc976edb76a918e8f

commit cdc4b34576d0d2a5b9391b5dc976edb76a918e8f
Author: Vadym Doroshenko <dvadym@chromium.org>
Date: Thu Jul 05 17:25:25 2018

UI code updates PasswordFormManagers only on deletion.

UI code should update PasswordFormManager on operations that are
initiated from UI but not from operations that initiated from backend.
Ideally it would be great that updates have information whether this
update come from UI (i.e. from the user) or backend. This CL makes that
UI initiates update of PasswordFormManager only when all updates are
deletion, now it means or the user cleared browsing data or removed
credentials in bubble.

In order to test this change, method UpdateFormManager of
PasswordManagerClient is introduced.

This CL fixes bug with deletion of pre-saved generated password on
editing. The details are on the bug.

Bug:  852430 
Change-Id: Ib9f00edba216d7e16ef3db39ea0dc54a537908db
Reviewed-on: https://chromium-review.googlesource.com/1118551
Reviewed-by: Vasilii Sukhanov <vasilii@chromium.org>
Commit-Queue: Vadym Doroshenko <dvadym@chromium.org>
Cr-Commit-Position: refs/heads/master@{#572822}
[modify] https://crrev.com/cdc4b34576d0d2a5b9391b5dc976edb76a918e8f/chrome/browser/password_manager/chrome_password_manager_client.cc
[modify] https://crrev.com/cdc4b34576d0d2a5b9391b5dc976edb76a918e8f/chrome/browser/password_manager/chrome_password_manager_client.h
[modify] https://crrev.com/cdc4b34576d0d2a5b9391b5dc976edb76a918e8f/chrome/browser/ui/passwords/manage_passwords_state.cc
[modify] https://crrev.com/cdc4b34576d0d2a5b9391b5dc976edb76a918e8f/chrome/browser/ui/passwords/manage_passwords_state_unittest.cc
[modify] https://crrev.com/cdc4b34576d0d2a5b9391b5dc976edb76a918e8f/components/password_manager/core/browser/password_manager_client.h