Originally Posted by masonos

You can do the following.

Stop rtorrent in both seedboxes.
On the NEW server run this:
rsync -avhSP --stats user@OLDSERVERIP:/home/user/ /home/user/

Of course change the user paths on both source and destination

Worked perfectly.

In case anyone else stumbles here as well. What I did after was copy the rtorrent session directory from the old server to the new one. It loaded up all the torrents then I selected all and changed the download located to match the new server. After checking all files, they're now seeding successfully.