I updated to UnRaid 6.12 this week with Channels-DVR and Plex running as Docker containers as well. These are working as expected.
I have no idea how it was working for you before. Channels-DVR should not have seen any files other than its own recordings that are stored in the DVR Database Storage Paths.
The Storage Paths in the DVR Database section is where Channels-DVR will store RECORDED movies and TV. this location also stores other data Channels-DVR needs like the logs and meta data.
Local Content is where you tell Channels-DVR where media that you've ripped from DVD's, Blu-Ray's or video's downloaded from your phone are located.
This is how I have my Channels-DVR Local Content setup.

These are the folders I have media stored in on my server:
/media/Channels-DVR
/media/Movies
/media/TV
/media/Videos
I point Channels-DVR's Local content at the bottom 3 folders and let Channels manage content in the first folder. For Plex, I have it look at all 4 folders. I only have Plex so my grown-up kids can stream my content from their homes.
As tmm1 points out, you should separate the content Channels-DVR recorded from the content you've acquired from other sources.
Technically, you could just point Local Content at the same folders that Channels-DVR is recording to. That would bring all that content into Channels, but everything that Channels recorded would show up twice in your TV client.
A better option would be to create new Movie and TV folders on your UnRaid server and move all the contents of those 2 Channels-DVR folders into the new folders. If you have home videos, create a Videos folder and sub folders in it for specific content. I have sub-folders for special events like vacations. Once you've moved media out of the Channels folders, then you need to somehow clear what Channels thinks it's recorded. tmm1 should be able to advise you on how to do that.