"However, since he did not paint 'John' as sketched in his notes, he must have had a change of mind"
This writer knows it is becoming repetitive to say, but it simply doesn't matter what "face" or anything else about the figure Leonardo decided upon relative to its final state. He still considered it a male according to the entry into his notes describing the interplay between the two male disciples he was going to paint.
It is well known, isn't it, that Leonardo would follow someone he saw in the streets, at a market and elsewhere to capture their "face" as well as using models? Isn't it also a matter of record according to his biographer Giorgio Vasari that he delayed painting the "face" of Judas in "The Last Supper" because he could not find the "right" face to characterize the 'evil' he had in mind to portray, even reportedly searching among criminals for someone after which to model Judas' face?
If, therefdore, he at one time sketched one figure in his preparation for painting the disciple John but later found a "face" that he preferred to represent the youth and innocence he had in mind and painted that
face in his final portrayal of the disciple, it still
represented a "he
" as far as he was concerned per his notes. Accordingly, it would not matter if the "model face" he ultimately chose was selected at random from a young male or female or one he had previously catelogued, it was still going to be a "male" disciple in his finished painting, again, according to his notes. There is simply nothing else that exists other than wishful speculation to suggest (much less validate) that Leonardo ever thought of the disciple's "gender" seated at Jesus' right as being anything other than "male".