Ah hah, so, I duplicated the vault via @rigmarole’s suggestion and gave the workspace a try, and everything came up clean and working. On a hunch I tested a few new plugins on this new vault and narrowed down the culprit.
I was using this plugin to get the column view in a few of the documents (not all of the ones that were disappearing, which makes the situation weirder), and as soon as I put it on the clean vault with no other 3rd party plugins running the problem appeared again. Strange how this plugin isn’t playing nice with workspaces, I’ll leave a comment on the Issues tab on github.
Thanks for helping me track down the problem! The troubleshooting helped a ton. :]
(also, thanks @Yurcee for clarifying the difference between the two files for me)