I'm in server that has designated areas for mining blocks that regenerate. I tried using mine but there are the same blocks outside of the area that cant be mined. So if I try using mine it will get stuck mining those blocks that I cant break over and over.

Making a selection doesn't work because baritone doesn't move to pick up the blocks and if it clears the area it wont keep breaking the blocks like .b mine does. Is there anyway to get around these blocks while still using .b mine?

Well, if there's the same blocks outside the allowed area and you can't use #sel replace you've got a problem without a solution.
Maybe you can reduce the blockReachDistance so far that it is always close enough to pick the block up?