As long as the changes in region A don't affect anything in region B, it should continue on as before the changes.
If you were to make changes to the main site for a region that has an active experiment, you will receive the warning "out of sync".
What happens if I do changes in Region A, while having an active AB test on region B?
As long as the changes in region A don't affect anything in region B, it should continue on as before the changes.