I have my laptop, my server and my usb drive. My server is a gcrypted remote via ssh. My laptop is just a repo that's referenced as a remote with a filepath.
I do git annex copy --to server, and let it copy stuff. I repeat the same thing for the usb drive.
I run git annex sync and it does the whole sync dance successfully. it pushes stuff to both the usb drive and the server.
Afterwards, I do git annex whereis, and I only get 2 copies showing - my laptop and my usb drive. Likewise, since I set numcopies to 2, it won't let me drop anything at all, because it doesn't know there's a copy on my server.
Anything I can do about this? (What further info do you need?)
I should probably add that my server is a ubuntu machine, and so it runs version 5.20140412ubuntu1. My laptop runs a more recent 5.20140717-g5a7d4ff.
To add further to this, the gcrypted remote does not show up in either the usb drive's git annex info, nor the laptop's git annex info.
Despite that, I can push to it and copy to it.
Sorry that it took me so long to get back to you.
The git remote that corresponds to your server should have an annex-uuid setting. (Eg, remote.server.annex-uuid.) Look up the uuid. Then look in
git-annex info. I'd expect the uuid to be listed there. It might be that somehow two repositories got the same uuid set (probability says no, but things find ways to break). If that did happen, I think it would replicate what you've reported, and in that case, the server's uuid would be listed bygit annex info, but perhaps it would have the name of the usb drive.