I was having trouble getting the DVR to recognize some new files I put in the Imports folder. When I clicked on Scan Sources, nothing was happening at all.
Then I accidentally deleted /media/DVR/Imports/TV from the TV sources ...
If /media/DVR is the primary storage location for Channels DVR, then you don't need to do anything. Channels will automatically scan the Imports/Movies and Imports/TV subdirectories of your primary storage location. You do not need to manually add them in the web UI; they are internally configured and already scanned regularly.
Correct. The locations you add for local content to import must reside outside of the DVR storage location. As I referenced above, the Imports directory in the storage location is already scanned, so you don't need to add that. If however you have other local content to add—such as a directory of movies you share with a Plex install—then that would be the place to add it.
You're not doing anything wrong, per se. In your situation it looks like the best option for you is to:
Remove the /media/DVR/Imports/Movies and /media/DVR/Imports/TV locations from the Local Content section.
Continue to put your imported local content into the /media/DVR/Imports/Movies and /media/DVR/Imports/TV locations for movies and TV shows, respectively.
That's it. Keep your content where it was, and Channels will automatically find it.