Slightly-related but I ran into a similar issue after rage alt+f4ing to preserve a kit, jumping back in to a raid (and dying), and some of my stash was missing.
Thought fuck it, it is what it is and kept playing and the next raid the items reappeared, both times in tarkov's console I saw an error along the lines of 'Error: Destroying multiple objects--' so I figured if the items are reappearing then it is just a matter of clearing space.
Seemed to have worked and the console isn't displaying an error anymore.
my hazardous guess in my case was possibly due to a combination of almost-full stash, autosorting and the alt+f4 right as a raid ended. Regardless it is fixed and I thought I should comment for the sake of documentation or whatnot. I hope Schepeppa was able to get theirs fixed.
On a side note, when situations like finding a bug, fixing a bug crop up is it worth writing up a support thread even though support is not needed? I'm just wanting to help but I don't want to clutter