Bug When overrides same as before, what is going on?

I'm constantly being shown a left and right that's the same, in objects I know haven't changed, other than to "upgrade" unity version.

Now there's hundreds, of used Prefabs in levels screaming out to have their overrides considered... even though they're not actually overrides. They were as they were, but for the "upgrade" of Unity.

Agree to override them only works on the individual instance. All other level/scene instances of the same Prefab are still crying out for their share of my override attentions.

What can be done about this?

Example:

 

What thoughts do you have on why this might be happening?

 

More important, what can I do about this, now!?

I don't have time, like everyone else not working for Unity, to wait for Unity to figure out how to fix this, and then roll that into a long distant future.

 

Thanks.

I'll write a script.

You guys should fix whatever causes this.