Given that repo1 and repo2 both have a branch adjusted/master(hidemissing), those branches should be local to the repo as they contain the files available locally. Yet, when doing a sync between the two repositories, the branches are forcefully merged which is wrong.

$ git annex sync
commit (recording state in git...)
On branch master
nothing to commit, working tree clean
remote: Enumerating objects: 332, done.
remote: Counting objects: 100% (332/332), done.
remote: Compressing objects: 100% (185/185), done.
remote: Total 232 (delta 35), reused 0 (delta 0)
Receiving objects: 100% (232/232), 20.46 KiB | 1.57 MiB/s, done.
Resolving deltas: 100% (35/35), completed with 2 local objects.
From /media/leggewie/WD250G/
 + 20bcd18...170148a adjusted/master(hidemissing) -> WD250G/adjusted/master(hidemissing)  (forced update)
   a071f8c..4a1f6d3  git-annex                    -> WD250G/git-annex
pull WD250G ok