I think formally, the fee should be waived where

1) It's a facility the website offers
2) The website is failing to perform the transaction

Which sounds like your scenario, so they should waive it. I think officially the fee is not meant to be waived if you need to phone up for something the website doesn't offer e.g. certain complex bookings where 1) doesn't apply, but in practice I believe many agents will do so anyway.

One more thing to check, is your ET booking in a class that is eligible for upgrade? (Q,O,G are not). I mean, why on earth would BA send you an email inviting you to upgrade if it wasn't, but c'mon, this is BA IT