how big a dose did you hit them with?
how old are the plants? which soil are they in and how big are the pots?
yes i would flush them, though if they're too small or too burned it might not work. but it IS worth a try!

I don't remember exactly the amount it was, but it was the portion the directions said for 1gallon of water.

The plants are a couple months old, the Jalapeno is already producing 4 small peppers, but the Habanero was just about to start producing. The pots are 5 gallons and each plant has it's own pot.

At what point do it just say... screw it i'm going to get new ones and start over? Thanks for the advice.

i was asking about pot size because if they are stressed by fertilizer, flushing them while in a gigantic pot with maybe soil that will remain wet for longer would stress them more and possibly cause further root death. but i think you have nothing to loose, just flush them with lots of water and then try to get them to dry out as fast as possible... if they were mine i would maybe even remove them from those pots, flush their roots, remove any rotten parts and pot them into smaller pots in some light soil until they recover. in the meantime i'd flush the soil in the big pots and leave it be until the little guys get back on their feet. but that depends on how the plants look i guess, if there's little damage i'd just flush, if they look really crappy i'd re-pot.
just throwing ideas, i hope you get them well again!