So yesterday morning I reran guided setup because my cable company got a new lineup and the new channels were not added automatically. After it was over it appeared to work, but some of the scheduling was off. (I was missing a bunch of stuff on Wednesday) I tried forcing a call and got a failed error. Tried rebooting, rearranging the SP manager, and a few other things but nothing worked. So I assumed the new lineup was corrupted so I did a clear guide data. Turns out all my problems were being cause by TiVo's servers being down, but I didn't know that at the time.
Anyway there were some really weird side effects from doing the clear guide data I wanted to report...
1) Everything in Recently Deleted was restored so my TiVo was now showing 100% full. I had to manually go through the list and re-delete all the stuff I had already watched.
2) All the recordings I had that were transferred from my Premiere were suddenly marked KUID. I never mark anything as KUID.
3) A couple of shows I had transferred from my Premiere which are not currently airing lost their grouping.
All of these were unexpected and really weird so I figured I'd put them out there in case TiVo decides to read this thread or to warn others who might be considering doing this type of clear.