Luckily git stash pop
does not change the stash in the case of a conflict!
So nothing, to worry about, just clean up your code and try it again.
Say your codebase was clean before, you could go back to that state with: git checkout -f
Then do the stuff you forgot, e.g. git merge missing-branch
After that just fire git stash pop
again and you get the same stash, that conflicted before.
Keep in mind: The stash is safe, however, uncommitted changes in the working directory are of course not. They can get messed up.