If you've switched from uTorrent to Torrentflux or vice versa, your files are still on your server.  Here's what to do to get your torrents up and running again:

1) Log in to your server via SFTP with your favorite client.  With FTP, you will not have access to the higher directory structures.  More on connecting through SFTP here.

2) Move your downloaded files from your previous client's directory to your new client's directory:

• uTorrent stores them here:  /data/admin/utorrent/
• Torrentflux stores them here:  /data/admin/torrentflux/admin/
• ruTorrent stores there here: /data/admin/rutorrent/
• wTorrent stores there here: /data/admin/rutorrent/
  

3) Move your .torrent files from your previous client's directory to your new client's directory:

• uTorrent stores them here:  /data/admin/utorrent/.transfers
• Torrentflux stores them here:  /data/admin/torrentflux/.transfers
• ruTorrent auto-starts torrents placed here: /data/admin/rutorrent/.watch  (Make sure your data is in the data dir before moving .torrent files here.)
  
• wTorrent stores there here: /data/admin/rutorrent/.transfers
  

 NOTE: You may have to create one or both of the destination directorys if your client is as-of-yet unused for downloading.

4) Now refresh your client and start your torrents.  Enjoy!

NOTE: If some of your files don't show up in your new client, look for special characters in your .torrent file names.  Spaces and certain special characters are not compatible with Torrentflux file names, so Torrentflux always renames them when adding through the web interface.  If you upload directly, you will need to check the names yourself.