Hi John,
I actually said we NEVER drill pegs holes until it's time to prep for the raising. I sure don't want that to infer that anyone who does is wrong. For us it's a precaution based on observation of what we have decided were our own mistakes. It seems the problems are worse with really green wood, but we have seen checks start to happen within days of drilling. The oval hole problem takes quite a bit longer, weeks at least.
I'm not sure of what the best solution is if holes have been drilled already. One idea would be to drive pegs thru the holes that could be taken back out before the raising. That would cut down on rapid drying along the end grain in the peg holes.
For oval holes, you could re-drill before the raisng, but be really careful. It's pretty easy to split the wood along the grain because the bit will tend to "rifle" into the already drilled hole. I would recommend a drill motor with the pipe extension handle, since the bit will want to bind and tear your arm off. The other option would be to use slightly undersized pegs so the pressure perpendicular to the grain is reduced. That would make splitting along the grain less likely at the raising.
Last tip, again based on my own mistakes, is to use parrafin on the pegs for holes in recycled timber and holes that were drilled well ahead of time. We like the blocks that are used for canning jams and jellies. It's a great job for kids at the raising. Just have them wax the tapered part and the pegs drive much better. Of course if the neighbor you invited hits them crooked they still break right off. But that's a different post.
Keep up the good work and as Lenny Brackett says "Cherish your mistakes. They are your best teachers!"
Rudy