If I recall on the KDX the filler is on the clutch cover side. Normally things on that side have to go up a hump and thru a small passage to get into the tranny. I'd pull the clutch cover off and look for the peice before firing it up. It probably won't cause any problems, but I'd get it out if it were me...
I had some metal down in mine and used a combination of diesel fuel and motor oil in a small sprayer and tried to flush things out. Tilt the bike towards the removed cover side and spray away. Pull the drain plug too. Run about a gallon thru it. Let it drain well, then button it back up and fill with oil.