I'm not sure how to articulate what I -think- has happened, but here goes. This is the most major of several bug issues I've been having.

While working on artwork, I haven't had much trouble saving files - apart from the actual method of saving, which is dangerously capable of tricking a tired artist at the worst moments (Like when an artist is repeatedly rendering finished images while also saving the document itself - nobody likes to find out they accidentally saved the last hour's work in PNG's instead of nice files with all their layers intact!)
However, I recently saved my file off a piece of paid work (!) - I had to do it a couple of times, as I wanted to make sure I was saving properly. I saved as new file; and just a little later, I saved over an old file as my latest copy.

I returned to open my file a couple of hours on, and my heart sunk. Instead of my recent piece, it was still saved over the much older copy - little more than reference shapes and shading info! Somehow, it seemed to have under-written the file - as in, it saved the old file over the new one - strangely, the thumbnail icon is displaying an intermediate stage with lineart, yet that detail is missing from the file itself.

After a mild panic, I found there was still a very recent autosave. Thank the Krita crew, for a decent autosave feature! Still, I'm trying to work out where my file went - no doubts that it saved, because the "new" old copy is a newer file than any of my others. It's got me worried about being able to work in this program in the future; a great program, but it is too risky for my tastes, to have my work compromised like this.

There could be some more useful details to this story, especially around the time of saving - but I can't remember, as I only found out when I came back to my work later on.



TLDR:

When trying to overwrite a .kra file I was working on, a very early draft copy was somehow saved over in place of the new one; deleting all of the work in the process.