Payment of £1000 taken twice

I recently paid £1000 online via the HMRC website towards an outstanding balance, and then set up a payment plan to cover the rest as I am undergoing a period of financial hardship. When I checked my bank account, there were two payments of £1000 to HMRC that had come out. I called HMRC to be told that it wasn't showing on their system yet, and to wait a few days. I waited, called again and have been told that I can't have made the payment. When I said that I hadn't, and that I only had a confirmation email for one payment, I was told that I "must have pressed the button twice" but as I owe the money anyway, I can't have it back. I've now spoke to my bank, who have given me a list of things to ask HMRC in order to try and get this money back, including the reference numbers of the separate payments. The bank's process takes 20 working days. HMRC will not give me these numbers unless I write a letter. I feel like I'm in some sort of Kafkaesque, authoritarian, dystopian nightmare. How can the state take £1000 from me and refuse to give it back, and then make it impossible to follow legal channels to get it back? I'm on a payment plan to cover the rest of the money, so why can't I have that £1000 back? Why would I make two payments of £1000 within seconds of each other? Things are difficult enough as it is at the moment without me being £1000 down. Has anyone else out there have a similar issue? Is anyone at HMRC reading these messages that can help????

Hi,
HMRC cannot forcibly take money from a bank account without the owner's authority, and without significant prior warning.
However, if you mistakenly sent this amount and will suffer hardship as a result, write to us at:
Self Assessment, HM Revenue and Customs, BX9 1AS, confirming the payment amount, the date it was paid, along with the bank details you would like your payment to be repaid to, and the reason why you need it to be repaid.
Thank you.