[[!comment format=mdwn
 username="joey"
 subject="""comment 2"""
 date="2020-03-09T17:46:31Z"
 content="""
You need to tell me a sequence of commands that can reproduce this problem.
At the moment, I don't know how to, and so don't know how to fix it.

If you don't know how to reporoduce the problem, you need to at least
more clearly explain it. I don't know what it could mean for a file to be
"symlinked from two directories". What was the full filename of the 
file that you deleted? What was the path in which you ran git-annex?
"""]]
