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 ok 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/@1TB.work + 20bcd18...170148a adjusted/master(hidemissing) -> WD250G/adjusted/master(hidemissing) (forced update) a071f8c..4a1f6d3 git-annex -> WD250G/git-annex pull WD250G ok