You can stash your working tree and then drop the old one that you don't need.
git stash apply
# Make changes
git stash
git stash drop stash@{1}
Alternatively, you can pop instead of apply, which will drop the stash at the same time:
git stash pop
# make changes
git stash
Another alternative, if you already were already making the changes that you want to do before realizing that you want to merge the changes to the top of the stash:
# make changes
git add <all files>
git stash pop # or apply
git rm --cached <files that you want to merge>
git stash --keep-index