It's been a while, so it's probably worth covering this again.
If you have ANY files that are in the batch, it's worth it to START the batch. STOP the batch. Copy/cut the files you already have into your torrent directory. Then START the batch over again so it rechecks for the new files.
The reason you'd want to do it this way is so that it doesn't download those files again and helps upload those files to the swarm.
If you were on the torrents that were deleted, please move your partial files over so that it can be resumed in the batch torrent.
Remember that with torrents, it doesn't matter if the file is corrupt. Torrents can patch files for you, so they're super handy.