[neallewis]

I suspect it's speculative invoicing...
Basically tell them to sing for their money. Don't pay them anything. If they have mistakenly paid a "random" amount of duty on your behalf, it's their loss.

They will "suspend your account" (which you may not even have) and send you letters demanding payment, which they may sell onto a debt collector or just write off after a year of sending you letters. Just ignore them, it will go away.
Most of their customs charge is actually their handling fee, with a tiny proportion in actual VAT/Duty. It's their error. Refer them back to the shipper, who actually paid them for the delivery service, and offer to provide proof of the actual cost of the item, which is sounds like you have.

I had a similar issue with FedEx who handled a warranty replacement gopro camera. It was a "no cost" replacement camera handled by GoPro in the US, though bought and paid for here (duty already paid). When they shipped it back to me it got held up in customs and the demanded I paid the duty on this camera I was importing. After battles with their customer (dis)service department and assurances from Gopro that it was a no-cost replacement camera they finally shipped it to me. They then proceeded to bombard me with threatening letters demanding payment of the customs duty and VAT and their handling charges, as I had imported a new camera. I ignored it for a bit, then a very very strongly worded letter with proof of the no cost warranty replacement made it all stop.

They are the shipping handler, you don't owe the HMRC anything, if you already have the item. It's their mistake and their loss.
I do wonder what will happen if someone ships something to you via DHL again however?