Can an app update from Play Store reinstate its permissions I've disabled earlier? There are quite a few apps out there that request too many permissions during install time, most of them seem  highly dubious. I tend to disable permissions I feel unlikely to be used and for the most part I get it right.

Can an update to said app reinstate its "factory" permissions that I've disabled? (an update might be from Play Store or APK)

This is about protecting privacy, which, I feel, is increasingly difficult these days.
Cases that doesn't affect your current permissions:


Updating app from play store.(also maybe the same for apk install too)
When you disable/enable any app.
When you clear only app cache.
When you force stop and restart.
During uninstall updates of an app. (This action is performed automatically when you disable that app).


Cases that may reset your current permissions:


When you clear Data and Cache.
During reinstall. 
After factory reset.


Note: The app developer/company can add more permissions while releasing a new update to a currently running app with specific permissions. 

For example, phone app have many permissions such as contacts, phone, sms, storage, location etc. But, we need to set these permissions only such as contacts, sms, phone. Later, when developer release app update he adds camera permission for video calling. User need to enable this for video calling purposes.