Atlas Map scarabs bug

I don't know exactly how to discribe it but basically I was using all 5 slots for scarabs and then I was doing the end boss of the Eagon Caeserius quest line where your atlas map changes its theme into like red with stuff flying around.
Anyways I had 5 stacks of 20 in and maybe did run 2-3 maps before the switch and now I wanted to continue but all the scarabs are gone.
I assume with the theme switch, all the slots were wiped.

I dont think it will help but here is a bug id from afterwards: 2978748531

EDIT: Nevermind, the game moved them into my stash for whatever reason. o/