After a bit of research, I found a solution to my problem - all of my databases were syncing properly, but the databases in question were in the DTTG app, but for the life of me I couldn’t figure out why these two particular databases were refusing to show up.
The short of it is that I changed the titles (not the actual database names, mind you) of these two databases to have a . as the first character, so they would always sort on top.
The Files app interpreted those leading periods as hidden system files, which are hidden by default.
Changed those to a different, unreserved blank Unicode character (⠀) and they’re back in the Files app under DTTG’s file provider extension (sorted on top as well!).
Just a little heads up if anyone comes across this problem in the future.