Most growers will tell you to flush before harvest, and I'm no difference. Flushing makes no difference when it come to potency that I can see, but it makes a HUGE difference on flavor. If you don't flush for at least a week (preferably 2, as everyone has said) your buds will have an unpleasant taste. Some saw it tastes like lawn clippings, but it just tastes like chemical burn to me.
Flush it and then chop, but if you're starting to get mildew you may have to cut your operation short early. If you have to chop, try and just chop down the buds that are showing mildew and get some extra fans blowing on the plants to dry the air out. Less moitsure in the air = less chances for fungus to survive.