This could be completely unrelated but my experience with vanishing fish from some time ago:
I have a base near the Mounds. About half way from portal to base I (had) a small fishing place (10 traps or so with just enough foundations to fill the timer)
The fishing place seemed to be just on the border of rendering distance of my base. Big base, lots of lights, at the time way over 100 thralls. Loading time was BIG.
Few times I noticed that when I jumped from portal and few (20ish) seconds later started to pick the fish and move them to my bearer, whole stacks would just dissapear regardless if I used mouse hold, double click or shift to split the stack. Traps were both normal and improved.
That never happened if I moved to the fishing place from the base (I was there long enough for everything to load I guess).
My conclusion at the time:
This was caused by general instability of the game while a nearby big base was loading. I simply revised my “fishing time”
Does that dissapearing for you happen always or “just” often? If not always, is there a chance that there is a nearby (your) big base loading? Or is there maybe some other patteren of events that you noticed?
As for repeating my “bug”: I dismanteled the fishing place (one independent purge point too many), started reducing the size of the base (hard to defend against purge without several players), and I prepared for the incoming thrall limit.