Can I check my luggage through even if I am changing airlines in Frankfurt/Munich?

In most cases your bags will be checked through to your final destination if your connecting flight is issued on the same Condor ticket but there are exceptions.

In some countrys, e.g. USA, Canada, Brasil, customs is processed at the first arrival airport and not your final destination. In these cases the baggage cannot be checked through. You must pick up your luggage to go through customs.