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.

It is clear from the posts that it is not possible to enter for an L permit holder to enter after 90 days. Does any one know the process on how to get a visa (?) or dependent permit/visa if the dependent had stayed out of Switzerland for more than 90 days. (Indian / L permit holder).
Thanks for your answers.

Same process as originally. You have to apply for family reunification and your spouse/partner has to apply for a Type D visa.

Thank you. Recently they have introduced a process of personal appearance in Swiss Embassy. Is this also required to submit all the documents ?

I assume so, but you'd need to check with the embassy/consulate to be sure.