yipe just did it today for a PHX / IAH trip... No fee payable though as it couldn't be done online...
Oh, that old chestnut again.
I believe the official line to be if you should be able to do it online but because the site is not functioning, they waive the fee. If, on the other band, the website doesn't have the functionality to make the booking/change, the standard offline fee applies.
I've had to pay once when doing an open jaw 2-4-1 and I've also had the fee waived in the same circumstances - so in practice it depends who you get on the day.