Hi Matt,
Thanks for that — I'm in pretty much exactly the same boat, although in my case it's Halifax, not Lloyds. But they're essentially the same banking group and I believe use the same systems. A look at the similarity of their Twitter feeds and phone numbers seems to confirm that.
I'm beginning to suspect the problem lies with Lloyds/Halifax, after doing an experiment... My iPad had Apple Pay successfully set up for in-app purchases. Tonight, I removed my Halifax card and it will *not* re-add. The iPad hasn't been restored or touched in any way. The only change I can think of since I added the card to the iPad has been the upgrade to iOS 9 (and then 9.01).
I find it hard to believe that ALL Apple Pay users aren't able to remove and re-add their cards. I'm sure there would be more activity on Twitter and these forums if that were the case. That leads me to point the finger at Lloyds/Halifax... In the meantime, I urge anyone reading this with a card from Lloyds banking group successfully set up in Apple Pay not to remove it if at all possible. If my experience is anything to go by, you won't be able to re-add it, regardless of whether you're restoring a backup or using an existing device.
In the past 24 hours, I have gone from having my Halifax card successfully set up for Apple Pay on my iPhone, Apple Watch and iPad, to NONE of them!
I too will keep pursuing this with both AppleCare and the bank.
Neal