SOLUTION - at 'least for now (and for S3/TiVoHD or newer users), as of May 2nd, until OneLink stops transmitting basic cable on channels 1-99 and/or you get a CableCard (at which point you at 'least won't have to re-run this setup)
I arrived at this solution thru trial and error, no thanks to OL or TiVo, YMMV... And it might only be a temporary solution if or until OL stops transmitting basic cable on 1-99. FWIW some of the OL reps gave me the impression that it was to occur in a matter of months; at which point you WILL need a CableCard to tune the encrypted 800 channels (and will likely have to put up with the $1.75 monthly charge for the card plus the $5 or $6 BS digital access charge).
Note: This is primarily for TiVo S3, TiVoHD, and Premium TiVo users. Series 2 users see note on the following post.
People who don't own a TiVo nor rent any boxes from OL will still need a DTA converter box (and OL will eventually charge for those too).
STEP I
Alright already, here's what you need to do... First you need to re-run the Guided Setup. To do so simply go to Settings (or Messages & Settings) -> Restart or Reset System -> Repeat Guided Setup. Just follow the prompts as usual and enter your pertinent information (WiFi SSID/password if you're using it should already be filled out btw, so don't skip ahead and start re-entering it if you don't have to).
Now, when it asks whether or not you have a CABLECARD it'll give you three different options: yes, no, and install later. You'll actually want to go ahead and select the last one, it mentions something about digital access as well IIRC (I'm doing this from memory so it's not verbatim). Basically what you're doing is selecting the lineup listing that's labeled Digital at Zap2It, same listing that TiVos owned by people using a CableCard automatically pulls in (hence why they haven't had any issues).
That's it, once you're at the last step you'll notice that it will properly recognize a basic cable channel and when you finish you'll have all the info for those channels in your TiVo Guide. Enjoy! But not so fast...
STEP II
Now, if you've ever messed around w/the TiVo much or noticed the intelligent (though not necessarily intuitive) way in which it handles channel lineup changes you may already know where this is going... This listing your TiVo is now using contains the info for all the basic channels as well as the digital & music channels past 100 and even the new 800 channels which you don't receive. The problem is that when the original lineup change to 800 occurred your TiVo may have already automatically re-arranged your Season Passes and even your manual recordings (if you selected a show to record rather than a time slot & channel).
Fear not, you don't have to re-program all this again manually... Just go into Messages & Setting again, then Settings -> Channels -> Channel List. Scroll down the list (using Page Down is the quickest way) and simply press select to un-mark all the channels you don't receive. If you don't have a CableCard that will include every channel past 100 I think, just unselect them all. After you're done you can restart the TiVo or just let it sit for a while.
I haven't fully tested this but I already did it for a couple of channels and my TiVo has already adapted... It may not reflect the change immediately, it's likely that the channel listed next to the Season Pass title may never even change (long-standing bug), but eventually the recordings on the To-Do list will reflect the correct channel (check the View Upcoming Episodes menu too, it's usually reflected there before the To-Do list even).
Again, I haven't tested this bit fully, but I believe that telling the TiVo which channels you don't receive should save you the trouble of re-doing any recording settings (even for manual recordings), just like the TiVo shifted them on it's own originally. Also worth noting is that channel 21 recordings were re-arranged for me before I even did any of this, I think it's because 821 never existed in the lineup to begin with, not sure.