I have tried manually flashing the 5.0 (LRX21L) -> 5.0 (LRX21R) OTA for the Nexus 9 and I get an error message that there is an unexpected difference. Anyone know why this will not work? Will being rooted prevent me from doing OTAs?
That's one reason, running a custom ROM is the other. Updating a custom ROM (with the update for a stock ROM) or rooting a phone that could have been modified due to being rooted, can brick the phone, so those are the first things the update process checks. Unrooting may leave enough garbage that it still won't update, and you'll have to flash a stock ROM first.