Name.m3u would be the file-based versions, i.e. playlists saved as M3U formatted text files somewhere in your storage, named as something like "PlaylistFilename.m3u". Those would be the best versions to use, and should get updated whenever J.River changes the contents.
Anything without the M3U extender is referring to an internal playlist (i.e. existing within the local database only) and the only way those would get created again would be if you used the Import Playlists function (which as you know should never be needed after the first setup). They can also be caused if you import Poweramp backups via the Import Settings/Data function.
If you want to reconcile these to match with any recently changed filesystems you can use the Rescan/Resolve Playlists option in the Playlists category view, but much better to remove any non-M3U playlists. Then avoid using the Import function again at all, and just let the background scanner find the real M3U files on its own.
Occasionally a manual Full Rescan in Poweramp might be a good idea if you are continuing to use syncing software, which are never the most reliable when it comes to flagging updates.
Andre