I concur with Koos - look at the
pictures on my blog of the port side bow marked up from the moisture meter survey showing what happens if the holes are not properly isolated.
As far as over drilling goes - there is room. You only need to expand the hole enough to provide an isolation layer between the fastener that goes through the deck and the balsa. If you have room to put on a hex nut and washer, then you have sufficient diameter to over drill, fill and re drill the original size hole.