Just to update anyone who might be interested. Just had a conversation with the Migrationsamt and told them my situation and asked them about the 3 month rule. They basically said it's no issue at all and were almost surprised that I was worried about this. They said that they typically send out a letter to the person's registered address asking if they still live there before canceling the permit.

I was always under the impression that the border agents are the ones that would notice the period of absence and stop you from entering.

Well, there is always a chance that border control does notice so I´d not want to run that risk if you are non EU.
Personally I have never had them ask for my permit, but then I am from the EU

Yeah, she's non-EU but also has a 1 year multi-entry tourist visa in her passport too, so hopefully one of the two lets her in.