What steps will reproduce the problem?

Running assistant in foreground on one repository that is paired to another repository, than killing it using CTRL-C and restarting it

What is the expected output? What do you see instead?

I get messages like:

(Recording state in git...)
# Auf Zweig master
# Änderungen, die nicht zum Eintragen bereitgestellt sind:
#   (benutze "git add/rm <Datei>..." zum Bereitstellen)
#   (benutze "git checkout -- <Datei>..." um die Änderungen im Arbeitsverzeichnis zu verwerfen)
#       gelöscht:    "path/to/file"
keine Änderungen zum Eintragen hinzugefügt (benutze "git add" und/oder "git commit -a")
Total 0 (delta 0), reused 0 (delta 0)
To ssh://stormking@git-annex-volyova-stormking/data/repository/
   4e2c631..911b80c  git-annex -> synced/git-annex

Already up-to-date.

Sorry for the german language, I'll try to reproduce it in english, later. After that, the symlinks for the file in the repository are gone. I can get them back by reverting the commit but things like that make me very nervous.

What version of git-annex are you using? On what operating system?

3.20130102 on Arch Linux x64