The prompt says:

The newest version of "Google Keep
- notes and lists" has been disabled
because it requires more
permissions.

It can now:
* Display notifications
* Know your email address
* Detect your physical location

(Why can't I copy-paste the dialog text??)

Still happening on a regular basis.

From out of band email thread, it sounds like this might be a duplicate of  issue 627522 , which has a fix in  53.0.2785.x. We can keep this bug open for a little bit to see if that new build fixes the problem.  

Reports on the internal thread are that this is still happening, even on builds later than 53.0.2785.x where  bug 627522  is thought to be fixed. 

The next time the problem occurs, it would be useful to do the following:

1) Don't re-enable the app yet
2) Open a tab to chrome://sync-internals, go the the Sync Node Browser, and find the entry for Keep in the Apps list. Copy that data. 
3) Grab a copy of the Preferences file from your user data dir (https://www.chromium.org/user-experience/user-data-directory), run it through a json pretty print (eg 'cat $file | python -m json.tool'), and find the section for Keep under the "extensions" dictionary and copy that. 
4) Re-enable the app (you can get back to the permissions prompt from the chrome-extensions:// page), and then repeat steps 2 and 3. 
5) Attach to this bug the data you got from steps 2 and 3, both before and after re-enabling.