I was clearing snow all day, my Goretex boots were soaked through and are stinking. What is the best way to ‘wash’ them without compromising their ‘waterproofness’.

Maybe use some warm ‘water’.

Just wash them with mild soap & water.

Mmmm I know what you mean about the “stinking” smell as my MT90 boots started to smell like cat piddle after a couple of snow soakings.

In the end I put them in a sink of warm water with some (can’t remember the exact ratio) dreft powder overnight.
Next day I rinsed lots in warm/hot water and dried out in the airing cupboard for 2 days.
The upshot of this is they have remained mostly waterproof (water flooding over the top excepted) and have never smelt of cat wee since 😀

neutrogena antibacterial boot spray wins over my stinky feet