Even if you weren't part of the scheme, the agent completed the checklist and you got your deposit back, plain and simple. They were responsible to ensure everything was in good order and since it was, you received your deposit back. If the landlord has an issue then they can take it up with the Estate Agent to get money from them. (I am sure it's a worthless claim anyway).
The whole reason why the scheme was set up was because of big, bad landlords in the UK. A lot of them (not all) will try every trick in the book to keep deposits or charge for no reason.
Note: Our landlord tried to pull a fast one on us, the lease stated a one month notice to leave the house which we gave her yet (30 days later) during the final walk through she pulled out a BLANK lease template which said two month's notice and said we owed her another month (800 pounds). Luckily I had the original copy of the lease which said one month. Basically we told her she was flipping mad and she wasn't getting a penny more from us.
That was just one of many things she pulled on us during our time in the house.
Please don't lose sleep over this. Stay firm and tell the EA that
they signed off and everything was fine as far as they were concerned (many weeks ago) that is why they gave you the deposit back so they can take up the request for money with the LL and pay (not you), it's been done and dusted as far as you are concerned.
Crossed with Meg's...good to hear that the scheme is automatic, so even better for you to get some support from it.