Welcome to Regensburg ;-), one of the towns I spend quite some time.

If it is your last segment, you can skip it without any problems. Done that a few times.
If you are rerouted you have the choice either going via MUC or other Airports - then no Problem in going to Regensburg.
If it is not your last segment, then you have to take the Bus, otherwise the other segments will be canceled.

For MUC-Regensburg you have the Choice of the Regional Train (operates every hour) or the Airport-Liner Shuttle. They operate Airport Transfers to MUC (and as well a bit more expensive to NUE). You have to wait a bit for other guest joining, but they drive you directly to any address in Regensburg.