Follow the advice in this thread if you are playing alpha 20 or older versions. From alpha 21 on things have changed. This is information from Jugginator, an internal tester at TFP:
QuoteI would like to add that actually deleting region files isn't supported anymore, and it can lead to issues. There is a regionreset command in the F1 console that should be used instead. "help regionreset" for the command list