The only time that even happened was with the first update after jailbreaking and unlocking had first been discovered. Didn't they just get functionality back later, anyway?
People are paranoid about it now: IT CAN'T REALLY HAPPEN ANYMORE.
Unless you're a complete moron and reformat the chip as NTFS. 😛
Pretty confident that my 2.1 to 2.2 was not going to be a problem. Restore and Update took about 20 minutes. No surprises, though I miss my JB apps...🙁