I’ve noticed that when deleting some of my old custom channels, the channel numbers associated with them don’t seem to get purged. Have I missed a setting, or is this normal behavior?
Have you tried delete and recreate database under settings, live tv dvr, guide data, maintenance drop down.
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No, I haven’t. I’m always a little scared of options like that. 
@Rice is correct. That's the way to get rid of the old channels in the guide database.
Won't hurt anything, it just reinitializes the guide database and fetches guide data.
Just did it. Thanks for the info…
I do that anytime I change things like add/remove, hide/unhide, favorite/unfavorite channels in a source.
It also triggers the scheduler to run through your passes, like the daily morning guide update does.
Good to know. I’ve never done this before, so I was probably long overdue…