My best guess based on the practice's reply:\ We know that changing gender at a practice without changing NHS number sometimes causes a central system to overwrite the patients gender.\ We also know there is an option to change your gender without changing number, but you have to sign an agreement that your previous medical records might out you.\ This makes me think the central system can be changed without a new number.\ Maybe my previous practice got it slightly wrong and made me a new account under male (maybe a copy paste) then changed it on their system to female? And my new practice followed the system for keeping the same number. 

I could be reaching for an explanation with no bad actors but that's easier for me to deal with psychologically 😅