Yes, if your team's policies say that you check in the code after your bug fix, go ahead and do that. If you aren't ready to check in or don't want to check in at this time, but are worried about losing work, you can always create another shelveset just in case (keep the Preserve Pending Changes box checked so you keep your bug fix changes).
Once you are ready, find and unshelve the shelveset. Just like getting the latest version from source control, VS will try to automerge the changes. If there's a conflict that it can't resolve, you'll get the same Resolve Conflicts window that we're used to seeing from time to time to manually resolve the conflicts.