Don't know what metal reinforcing rod you are talking about, but in the pics below is a knackered and a brand spanking new side skirt/lower door fin. I guess it's possible to to remove the nylon runner with the brass inset bolts intact complete, then pull the rubber part out and refit the nylon runner with silicon as the filler/substitute for the rubber part. I highly recommend you go back to Audi and purchase the correct screws before refitting. They are 18p each, and you need 4 per side. The reason being, the original bolts - on my car at least - have iron content, and will rust away, aswell as being magnetic to some screwdrivers. The new screws I got are galvanized and don't magnetize, so you need a stead hand to feed them through the holes when refitting.
As for dropping the screws dropping into the door channel, just remove the doorcard(5 minute job once you know how), and you can get to them with a pair of long nose pliers.