You experienced first hand the results of mixing disk shares (/mnt/diskX,/mnt/cache/,/mnt/<poolname>) and user shares (everything under /mnt/user)
/mnt/user normally merges all the identically named root folders on all the disks into those named user shares. Since they are the same files and but appear in different paths, linux doesn't understand what you want to do when you copy between them, so it ends up overwriting the files with zero byte files.
So, to move files from disk to disk, use the full disk paths. To move files between user shares, only use /mnt/user/* paths. Don't mix the two.
You can try doing a recovery, hopefully you will be able to get your deleted files back.
This is the reason disk shares are disabled by default, with a warning in the help text for disk shares. Using mc allows you to access things not normally exposed.