I'm just writing this out for the sake of other people.
The easiest way that I've found to go about it is storing your primary save somewhere else and creating a new save with your preferred gender/appearance before opening that save in pkhex and exporting specific blocks before importing this in your primary save.
The three important ones are: Object Mystatus, Object PlayerAppearance & Object PlayerFashion.
Once you've exported those it's just a simple matter of replacing the blocks of your primary save.
There's also a decent chance this deletes all your clothing, but it's pretty easy to get it all back with pkhex with the "Unlock All Fashion" button in Trainer Info.
I'm just writing this out for the sake of other people. The easiest way that I've found to go about it is storing your primary save somewhere else and creating a new save with your preferred gender/appearance before opening that save in pkhex and exporting specific blocks before importing this in your primary save. The three important ones are: Object Mystatus, Object PlayerAppearance & Object PlayerFashion. Once you've exported those it's just a simple matter of replacing the blocks of your primary save. There's also a decent chance this deletes all your clothing, but it's pretty easy to get it all back with pkhex with the "Unlock All Fashion" button in Trainer Info.