I’m really enjoying watching my YouTube videos from within Channels. That said, there are a few issues/questions:
• Is it possible to trigger or automate Channels to prune deleted items from watched folders? Otherwise, I need to remember to periodically trigger this option to avoid clutter of deleted videos.
• Is it possible to hide watched videos as that would be a huge help?
• Can you manually sort the playlist of videos as I only see 3 options, but manual isn’t one of them.
Thanks 
It is not. This is a property of a Series Pass. This is something we've wanted to adjust for a while since adding local content. Hopefully we can make this better soon.
If you mean because you are deleting the video files from somewhere else, this is a bad idea and you're always going to run into this. We suggest managing this from Channels.
No. But please describe what you want to do with this, so we're more clear on what sort of behavior you're looking for.
You can not. But you can number videos with Season/Episode numbers just like TV shows and probably handle this that way.
Thanks for the replies. That said, being able to delete has solved most of my issues. Since these are YouTube videos and are temporary, creating a custom naming convention, probably wouldn’t make a lot of sense, especially as I like to order them based upon the content of the videos. It would be wonderful if at some point in the future, we would have the ability to adjust the play order.
Thanks again for your help
One more question for clarity sake. When I delete a watched video in Channels, it is not deleted on the server, is this normal behavior or do I have a permission issue?
Sounds like a permission issue. Check the log on your Channels DVR Server web admin, it would show an error.