This is something I've actually already gotten through, but it seemed really weird at the time, so I'm posting here in case someone else has the same problem down the line.

The problem was I had a directory that had been renamed in DOSBox that was showing up in DOSBox, but not in the host's (Linux Mint 20.3 MATE) file manager or terminal. Even weirder, there was a directory with the old name and some of the old files showing up. After scratching my head about that, I thought to look in some game directories where the game would have at least written a config file recently. Nothing from the last year or so showing up in the host file manager for those game directories.

Okay, now that's really weird.

Well, I tried the obvious solution of just quitting DOSBox and restarting it. Nothing. Also tried copying a file inside it. No show outside DOSBox, even with another restart.

Then I try searching for solutions, and come across a bug report for the opposite problem. Someone couldn't get files copied into DOSBox mounted directories to show up in DOSBox. The suggested solution was to type "rescan" in the DOSBox prompt. It worked for them, so I figured "Why not?".

I tried it in my situation, and SUCCESS! Two mirror-image problems with the same solution.

Somehow DOSBox and the OS managed to maintain two different views of the file system that were preserved between DOSBox sessions, and multiple hibernations and probably host system reboots, too. I don't know how it happened, but hopefully this will at least provide an answer for someone who comes looking in the future.