I think I have run into a similar problem to you. I originally filled in a tax questionnaire in 2014 and did so with an EIN issued by the IRS.
When I went to re-submit my details in late 2017 the IRS rejected the new form. Amazon told me this was because my details were different, but didn't give me much of any guidance on what was wrong.
I finally learned from them that, while I was entering the same EIN as in 2014, I was wrong to do so because, as an individual I should have been submitting a Social Security Number or an ITIN (neither of which I have, or should have, as a foreign citizen).
I then spent ages trying to find a way to re-submit an EIN as an individual owner / sole proprietor, to no avail.
My guess is that I should be entering a UK tax ID, as you did.
So, here's my question ...
When you went back and completed the questionnaire successfully, did you only enter a UK NINO (or UTR)? Or did you also include the EIN that you included on the original (ie, pre-2017) questionnaire?
I am at my wits' end with this, so any advice you can give me would be a huge help,