When I've had flights changed by WN because of schedule changes, I was told that EBCI had to be manually added to the new flight by the agent. (Unlike when you change a flight yourself, where the "rule" is that if the PNR survives, the EBCI should as well). I assume this is because of some nonsensical limitation of their systems. When that happened, I couldn't verify that I still had EBCI, because the flight was no longer accessible by me online after it had been touched by the phone agent.

You should have received an email telling you of the flight change -- did you?

I'd be shocked if the EBCI fee is automatically credited. You'll most likely need to contact them.