My question is, can you use a ds flashcart in emunand? And if yes would this leave the ds mode exploit intact?

If it was successful (which I'm not sure that it would be unless you swapped the carts with the power on and emuNAND already runny), you would most likely have to reinstall the exploit as playing any DS game messes up the exploit.
if the exploit gets messed up, can you simply just reinsert the blue card, install gateway again, and then regain access to the emunand just like it was before? i system transferred to an emunand so im just wondering if running a ds game would completely reset that emunand.