My clay mines remained paused despite production limits not being met (or even disabled entirely).
Both regular and a single deep one.
I eventually found solution, which is to set production limit to 0, run game for a few seconds, then revert to original production limits. This will reset the situation and everything works again.
I would upload save but I think all my saves are in the cloud. My steam account id is 81807518. The bugged save file is named durrington_bugged_mine and should start centered on the bugged mine.
edit: here is drive link, hopefully it works: