Once you add a second drive, it always expects that drive to be there and will not boot without it.
I've never tried divorcing a 2nd drive myself, but from what I have read in the past on the forums @ Dealdatabase it seems to be mainly unsucessful. I'd suggest doing a search there to see if a better way has been found.
It may be best for us to try and get the 2nd drive working for you.
One common thing is not setting the jumpers for master and slave on the drives. TiVo does not use cable select.
If it's not that, then post more details here about both drives and what occurs when both are installed.
Peter
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