A sort of temporal "buy back" system could be cool. Any despawned items, regardless of the cause, could be bought back using temporal gears. Like a trader, but with a buy inventory of items randomly selected from what has despawned in the world. Trade in temporal gears to get the items back that are most important to you.
Then item despawning could have some amount of "in universe" explanation as them getting lost in the temporal instability or something like that. And you're using the temporal gears to restabilize them out of the ether.