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One (Standard Def) series that has been recording with the CCI set recorded last night and now doesn't have the CCI set.

I tried MRVing to an unhacked TiVoHD and it showed a progress bar, but...

I have the same setup and same symptoms. TiVoHD to TiVoHD

That broke unhacked S3 to hacked S3 MRV.
It also broke hacked S3 to unhacked S3 MRV.

S2 to S3 MRV seems to work fine.
S3 to S2 MRV seems to work fine.