I run a server and have a 2.5TB repo on a 4TB drive. Right now I have a bare repo for outside connections on it, but thought about a non-bare repo beside this on the same drive for local use. Does git-annex realize the repos are on the same btrfs-volume and uses cp --reflink while syncing between them?
It will not realise this.
Why do you have separate repos for this though? You can absolutely just use a non-plain git repo for synchronisation purposes too.
synced/branchnameherebranches. The actual checked out branch in the worktree will only be updated when you run amergeorsyncin the worktree.