Answer: git remove file from stash, nice workaround

There is a workaround for this situation:

1. save your stash as a patch file:

   $ git stash show -p > stash.patch
   

2. apply this patch, skipping the conflicts (you will be asked for resolution of conflicts, just skip missing files):

   $ patch -p1 < stash.patch
   

Don't forget to clean up stash.patch…