Been meaning to share this tale of woe. Back around the end of October, Comcast decided to assign new channel numbers to all HD channels in my area. My friend got a notice in the mail regarding the change and gave me a heads up. I don't recall ever getting notified.
A few weeks later I got another call from my friend stating her HD channels got reassigned but her TiVo Premier box could not tune the new channels. Comcast apparently forgot to mention to TiVo that they were reassigning all HD channels. It took several days before TiVo sent out an updated channel list. To further complicate matters, Comcast made the change to different parts of town over a period of weeks. So my TiVo box got the new channel line up before the channels actually got changed. I figured at least there would be no service interruption.
Once Comcast made the change to my area, my TiVo box had the old and new channel list. I went in and removed all the old channels and restarted the unit. However, SPs were still set to record from the old channels. Gave it a day and another restart but the Season Passes were still set for the old channels. I contacted TiVo support and was told there was no solution and I would have to recreate all SPs (which it turned out was not entirely true). So I recreated most SPs and deleted the old ones but left a few untouched.
I then noticed that any Wishlist searches set to auto-record were also recording from the old channels. However, if I listed upcoming shows it was finding them on the new channels. So I turned off auto-record on all WLs, waited a day, then set them to auto-record again. When I looked at the To Do List, all the WLs were still set to record from the old channels.
I contacted TiVo support again. The CSR thought that manually deleting the old channels from the channel list should have resolved the problem but obviously, it did not. He went off to speak to the next-tier support. When he came back he confirmed what I concluded - TiVo would need to send deletions of all the old channels to remedy the issue.
Within a few days I received a line up change notice that all old channels had been removed. Sure enough, the To Do list indicated that the auto-recorded Wishlists would now record from the new channels and the old Season Passes I did not delete magically changed to the new channels.