Deleting a .torrent file will not affect any torrent that is still in your torrent queue at all, whether downloading, seeding, or paused/stopped. It's advisable, however, to keep your .torrent files for 3 reasons:
- Restarting torrents that you have removed from the queue, either on purpose or by accident (it happens more often than you might think).
- Keeping a record of torrents you have downloaded in the past. Every client that archives .torrent files will let you know if you later attempt to restart that torrent, whether by accident or on purpose (to add trackers).
- Restarting torrents after you have moved them to a new location. There's a number of other ways to do this, but having the .torrent files can make it a lot easier, if you're moving a large number.
If you really care to, however, you won't break anything by deleting the .torrent files.