As it turns out, Git is smart enough not to drop a stash if it doesn't apply cleanly. I was able to get to the desired state with the following steps:
- To unstage the merge conflicts:
git reset HEAD .
(note the trailing dot) - To save the conflicted merge (just in case):
git stash
- To return to master:
git checkout master
- To pull latest changes:
git fetch upstream; git merge upstream/master
- To correct my new branch:
git checkout new-branch; git rebase master
- To apply the correct stashed changes (now 2nd on the stack):
git stash apply stash@{1}