> running git-am on the isolated commit

Huh? That command just turns the working copy into a commit, and mark it as the unique descendent as the commit currently pointed to by HEAD. Worst case, you just created another branch (happens if HEAD happens to point to something other than the last commit of an existing branch).

You wouldn't happen to try and save the state of one branch in the working copy, then using that working copy to update another branch, right? That's just asking for trouble: done naively, it'd cancel all changes made in that another branch.

If you know anyone who did this kind of mistake, do them a favour and explain the difference between a commit and a patch.