Can an app update from Play Store reinstate its permissions I've disabled earlier?
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.