This is probably a silly question, but I didn't want to just try it and see if it worked before asking someone.

If I have a batch of images exporting for proofing, can I go back into the main folder of images and make selections and apply presets for slideshow images? Should I just leave it alone and let it work?

You can keep working, it just might be unbearably slow depending on your computer hardware. It's a factor of available processing power and disk access.

ive got a bit of a dinosoaur puter in terms of todays technology (even though its only 3 years old ) and ive done up to 4 different exports/imports/workflows at the same time in lightroom and while it does slow things down a little, its not enough to stop me form working efficiently.

On my old computer it would take forever just to have an image load, so while I exported, I usually took a break... for a while. BUT, I just bought a new 'puter and now I can do many things on Lightroom at once! Makes all the difference. In fact, it took about 2 weeks of torture to get through a wedding, and now it takes 2 days.! So if you find it to be really lagging, I would totally recommend considering a new machine! Mine cost $850!

I can export a whole wedding to large PSD files, play a graphics intensive game and listen to itunes all at the same time on my 8-core mac pro with 10 gigs of RAM....

.... your results may vary.