Any question answered...

I'm assuming a proper job, not just chewing a bit off in situ with an angle grinder...

Strip down to a bare axle, fit a (possibly sacrificial) nut below the anticipated new end, mount in a lathe, remove excess material, chamfer end, remove nut, repeat at other end.

If you have the correct die, this could be used instead of a nut - removing the die or nut after cutting and chamfering should correct any deformation of the thread caused by cutting.

The unwanted material could be removed by repeated facing off using a carbide tipped tool, but I've had good results from mounting a Dremel with cutting disc on the cross slide - slower, but less clamping force needed at the chuck and so less likelihood of distortion.

With care, patience, a hacksaw and smooth jaw engineering vise, you could trim the ends manually - not everyone has access to machine tools - the trick with the nut to re-form the thread would be essential in this case.

If it is only a few mm, I'd consider living with it. I've shortened a BMX axle because I have no use for stunt pegs, but Mrs.E described it as engineering OCD...

Depends how dexterous you are with tools.
I would use a powerfile if it is just a couple of mm. Or a large smooth hand file, taking care not to put the filings into and onto the hub.