If the map marker says "Cleared" below it you need to wait 30 days, if it does not you just need to wait 10 days in another cell (a player home is always a good choice for this).
Right now the ebony andnmalachite mines are glitches. They look respawned but I cant mine them and I clip right through them
Actually this happens with all mines (at least in my experience) and all you have to do to fix it is go out of the mine then go back in.