Not sure if this has been discussed before. I searched for “files disappear” and could not find anything relevant.
I understand that the system folders all get reset when the AppVMs are rebooted. However, I thought the home folder contents should remain. I rarely reboot my qubes machine because it is so stable running on 128GB of memory, but I have found when I do, I have had files I have created under my home folder completely disappear. Most are still there, but some such as some website captures I had done while browsing which I thought I saved in a subfolder under Documents are just missing, and I went through my entire home folder and could not find any of them. I bunch of documents I saved in a completely different AppVM that were saved under Documents are also missing (ironically the only ones remaining are the two Untitled 1 and 2 documents I forgot to save). No now I am a little nervous to save anything in Qubes at all.
I am not sure if this is related, but Thunderbird repeatedly crashes after a long period of use. When I reopen Thunderbird afterwards, or if I reopen after the AppVM has been restarted, my default profile is completely gone and starts blank. The default folder is still there, but I am guessing some files underneath might have been randomly deleted as well, and might even be the reason for the crashing. I literally have to reimport an old profile fom my server saved in QubesIncoming (that file seems to stay put) and redownload all my emails every time I Thunderbird is closed or crashes.