git annex sync - not pulling in files

I haven't synced my git annex repositories for quite some time and was trying to synchronize them recently, but am getting an error which indicates I need to merge. I am getting the error: Updates were rejected because a pushed branch tip is behind its remote counterpart. I tried to run git annex merge and git pull origin master, but git complains that I need to run it in a work tree. [EDIT] I fixed that issue I believe, as my shell command was set to git-shell. Once I switched to git-annex-shell, it seemed to fix that issue. Now, I noticed that I have some files missing even after I have done a sync and a get. I added both repositories to the other so repository A has remote B and repository B has remote A. However, even after attempting to sync and get several times, I see no changes. Those files are still missing in one repository.