So your SLT lied to you essentially - even if by omission. This is taking away parental rights which the school has no right in law to do. This is so anti safeguarding it's unreal (though not your fault - you were lied to).
I hope you told the parents this wasn't a decision you made but something SLT told you to do. I'd be looking for another job, the atmosphere must be toxic. In future if requested to use wrong sex pronouns please ask if the parents agree before doing this.
Also, it's really harmful to non English speaking children and non NT children - and all children actually - to mangle English in this way.
Third person pronouns are not parts of language that apply to an individual - like names. In common English usage throughout all of recent history (and beyond probably) they are determined by the speaker and refer to sex class as observed or determined by other means (e.g. via written material). The neutral 'they' is used if sex class is not known. If you make pronouns a matter of choice by individuals, like names, it renders them essentially the same as names, so you might as well just use names as at least this is more neutral and not a very obvious signing up to a particular political ideology.
It's very confusing if you're using one rule for third person pronouns for some and common usage for others - and it's arguably unfair and discriminatory. If the school is using gender based pronouns now they need to give all children a chance to determine their own pronouns otherwise they are treating some children preferentially.
Also, English lessons need to be changed and a discussion had about how all of the literature of the past (up until recently and even now for most things) uses sex class to determine third person pronouns rather than being individual and gender based and a clear distinction and announcement made where third person pronouns are sex-class based and speaker / writer determined or where they are individual, gender-based and determined by the person being spoken about. Anything else is incredibly confusing for normal children let alone children with SEND. It's not teaching the basics of English properly to just mangle the rules and not explain it.
It's like saying for some children 2+2=5 in Maths lessons and no-one must question why this is so but just blindly accept it and the fact that the rules are shifting and no-one can possibly know when 2+2=5 and when 2+2=4 but must just guess or stay silent out of fear of getting it wrong.
The Psychological impacts of this authoritarian behaviour on the other children is going to be profound.