Weaknees have some nice details on how to use the TiVo selftest features:
The one relevant to us is the 'TIVO HD/TIVO HD XL' set of instructions.
Amongst other stuff, this allows you to force your TiVo to reinstall the OS, to do a Hard Disk media test, and to check and fix the filesystem in case of damage. This all takes effect pretty early in the boot process so bypasses any other disk corruption.
This might be a good place to start if you're getting playback problems or reboots during playback, since a disk check and then FS fix could sort out issues. Look for kickstart functions 52, 54 and 58.