I might have found the reason, which is me
I think I happened to mechanically leave the saving menu when the overwritting message appears, thinking it actually was the "Project successfully saved", which led me to not save the project at all. I just surprised myself doing it so I suspect this may have been the cause for previous cases.
I use the Octatrack a lot and it has a quick save key, so saving is way faster on this one, I just need to get used to the way it's done on the Tempest I guess.
I'll let you know if this still happens but I'm pretty sure it was all because of me