My VaM folder has always been in an external drive.. nothing about that has changed in the 3 years I started to use it lol.. although when I restarted my computer the other day. I got an error message about that drive.. I restarted it again and at restart, the Bios start up did some sort of check to that drive. its 8 terabytes, so it took a few minutes. The only thing that was different was this.. but that issue with it forgetting what I had hidden occurred before the start up fix anyway. I wasn't in any folders that could have accidentally deleted that setting and I'm not even sure where that would be anyway.
edit.. since this post.. when I was In VaM this morning. i noticed all the favs and templates were gone too.. not just the hidden vars..
non of the files are missing.. just whatever linked the associated tag to hidden, fav or template is missing. Additionally and probably related in some way, the last time I opened up a scene that had a subscene, the subscene wasn't saved. everything was in the scene. but the subscenes wasn't saved in a folder like I had it previously either.