UserAgent: Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/58.0.3006.0 Safari/537.36

Steps to reproduce the problem:
(0) Login to your google account, to enable sync of chrome settings
(1) open chrome://settings 
(2) set Search engine to "Bing", then able to see "Bing" on New tab page
(3) install extension wich override default search engine - for example Yandex search https://chrome.google.com/webstore/detail/%D0%BF%D0%BE%D0%B8%D1%81%D0%BA-%D1%8F%D0%BD%D0%B4%D0%B5%D0%BA%D1%81a/laddjijkcfpakbbnnedbhnnciecidncp?utm_source=chrome-app-launcher-info-dialog
(4) make sure new tab opens with yandex page
(5)  open chrome://settings,  click on "Reset settings".  Then, "Google" is reset to default search engine on NTP/chrome://settings

What is the expected behavior?
Expect that google engine is propagated to sync and other devices.

What went wrong?
synced_guid in profile prefs still corresponds to search engine that user choose on step 2 (Bing)
Other devices will not receive google search engine with sync.

Did this work before? No 

Chrome version: 58.0.3006.0  Channel: canary
OS Version: 6.1 (Windows 7, Windows Server 2008 R2)
Flash Version: 

Similar to
https://bugs.chromium.org/p/chromium/issues/detail?id=680197
Only with extension search engine and user search engine.