To be more precise with regards to step 3 (clearing browser cache):
The issue occurs when only default check boxes are set in Chrome's cache clearing dialog (see attached image). However, when additionally checking 'Hosted app data' then everything works fine as expected. Furthermore, I experience the same behavior on Mobile Chrome on my Android (6.0.1) mobile phone.

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	chrome_cache_clear.jpg 43.6 KB View Download

When "Cookies and other site and plugin data" is checked, Indexed DB (and other site data) is cleared.

What you describe is what I'd expect if you had no "upgradeneeded" handler when opening the database after clearing. For example:

(1) execute this script:

var r = indexedDB.open('db');
r.onupgradeneeded = function(e) {
  console.log('upgrading from', e.oldVersion, 'to', e.newVersion);
  var db = r.result;
  db.createObjectStore('s');
};
r.onsuccess = function() {
  try { 
    db.transaction('s');
    console.log('ok');
  } catch (e) {
    console.log('no such object store');
  }
};

(2) clear browsing data

(3) execute this

var r = indexedDB.open('db');
// r.onupgradeneeded = function(e) {
//  console.log('upgrading from', e.oldVersion, 'to', e.newVersion);
//  var db = r.result;
//  db.createObjectStore('s');
// };
r.onsuccess = function() {
  try { 
    db.transaction('s');
    console.log('ok');
  } catch (e) {
    console.log('no such object store');
  }
};

Note that in the second code block there is no "upgradeneeded" handler; the database will open but no object stores will be created. This sounds like what you're observing, and is the correct behavior for the API.

Can you provide example code used before/after clearing that demonstrates the problem you're seeing, if it doesn't match the above explanation?

At first: Sorry for the inconvenience. 
I figured out what caused the issue: In my application there is only a startup check of whether a database upgrade is needed. However, there is a 'beforeunload' handler on my page for storing current application state in indexedDB to be able to restore the state on next startup. Now, when I clear the cache (database and its objectstores are gone) the 'beforeunload' handler is triggered trying to open the respective database objectstore without having set an "upgradeneeded" handler and then ... CRASH.

Thanks for pointing in the right direction and sorry for wasting your time. This way, I guess the issue is solved (no bug just a dumb user).

No problem - glad to help!