I have one more option for you to try: disable all of the channels on the HDHR tuners (from within the HDHR's own webUI). You can still tune them directly, so your M3U playlists within Channels will work, but Channels will see that the channels have been disabled, so it will not display them or attempt to assign guide data to them.
(If you are using AppleTVs, it would be best to delete the app from your device, make this change, and then re-install it. Settings, including channel states, are preserved on the client and don't reflect changes made in other places. A fresh (re-)install will ensure that no old settings are retained.)
Otherwise, I'll reiterate what I previously stated. Move your tuners onto a separate subnet, or block port 65001 via your firewall/router. Either option ought to result in your expected behavior.
I can certainly understand the goal you are trying to achieve, but you are obviously running into edge cases because you are not quite using the software as designed. When remapping channels I never ran into this problem, but that was probably because I was not trying to reuse a channel number supplied by a physical tuner.
Also, one good rule to adhere to when making changes to your lineup, changing channel numbers, adding/removing sources, etc.: after you have made a change, restart the Channels DVR server process, and then within the webUI do a "Delete and recreate guide database".
(Edit: port number was off by one.)