I searched around for a solution to this but I could not find one. I need to go through this place for the main quest but I had already gone through it earlier, dislodged all the things caught in the gears, and got out. Now I'm back in the gear room and they are stuck again but this time they have nothing lodged in them. I can't remove anything at all. I tried going around to the exit but for some reason it closed the door back up on me. Is there a work around for this? Has anyone else ran into this?

Thanks for any help.

I also ran into this issue. I stumbled upon Raldbthar relatively early in the game, and cleared it to find that I lacked the artifact necessary to activate the mechanism located at the end of the dungeon. Now, later in the game, I have obtained said artifact, and I ran through Raldbthar again to use it. Everything in the dungeon appeared to have been restored, however, as you mentioned, there were no bones stuck in the gears in the Deep Market. This makes the mechanism at the end of the dungeon inaccessible, and I have been unable to find any workarounds. Hopefully this issue will be addressed in a coming patch.

Okay, the only way I've found to fix this is to use console commands to turn off clipping. To do this just press the "~" key and type "tcl" and press enter, then go through the door. Make sure you turn clipping back on. I went through the exit located above the entrance, but you might be able to go through the bridge in the gear room using the whirlwind shout, I'm not sure.

Can't you go back in through the exit now that you unlocked it from the inside? The elevator that takes you out near the inn behind the mountains?

There are other entrances to Blackreach. At least the one at Alfthand doesn't require fiddling with anything to get in so it should always be usable.

No, like I said it reset itself and closed, I'm not sure why.

Ah, I didn't know that, thank you!