Leaving and returning to Munich airport after long layover

I would contact Swiss (or whoever you bought the ticket from) about whether the luggage will be checked through or if you have to collect it. Since Basel to Munich is inter-Schengen flight, no passport control exiting the airport.

While you won’t need to go through passport control when you arrive in Munich, you will need to go through passport control when you are leaving Munich. I thought that was worth pointing out.

Generally with Star Alliance carriers I have not had any problems through checking my luggage. You will get 2 boarding passes when you check in since you are on 2 separate flights. If you do check luggage through overnight, I would suggest you stop by a check in desk to make sure your luggage gets on the 2nd flight.

Will we have to retrieve our checked luggage in Munich or can it be checked through?

Did you buy your trip home as a single ticket or was it two purchases?

If the latter, you will need to retrieve and recheck the bag(s). { as Alliance/codeshare partners you might get them to check them through, but even then there is the issue noted below}

If the former, you may have to retrieve them as the airline/airport may have storage capacity issues of keeping bags for so much time. Need to check with the airline. ( as Sam mentioned )