Further to the post on sanding without filling, can anyone tell me if using the nail varnish method will cause canopies to fog up.
If it will,whats the best way to clear the canopy afterwards?

Nail varnish? I presume you mean nail polish remover?
That stuff contains acetone, which is more fierce than turpentine. It will most likely mar clear parts. Try it on some sprue to find out how it reacts.

If you already got some parts ruined, dipping them in future might help if the damage isn't serious.

Sorry,,I do mean nail polish remover.
I havent fogged a canopy yet I was thinking ahead.
Would an overnight soak in Future/Klear beforehand minimise any fogging?

Overnight soaking isn't required, just a quick dip. You dip the parts in future and let them dry in a dust-free environment on some tissue, to absorb extra future to prevent too heavy a coat. Remember to let the parts dry for a couple of days just to sure the coat has hardened properly.
This article explains the procedure and other uses for future as well: lThe future is klear
I've heard that future-coated clear parts resist the fogging caused by super glues, but I don't know about thinnners.