Assuming we are talking about the ribbing that's riveted directly to the Hull/sheeting.
Those I did my best to re-use holes, but it's not going to hurt anything if you need to make new ones.
In some places I did my best to use the same holes, but if it didn't look right i might add a second one for good measure (if possible).
I figure you're using Guvit to seal up the hull before assembly anyways?
I wouldn't think too hard about the bits that fall into the holes, just looking at how these things were assembled from the factory makes me think of something my grandpa would say.
His company specialized in bridges, and building roads.
"You're building a bridge not a piano."
Or in this case
"You're building a boat not a Piano."
The hull on my starchief had a "tilt" to it, they had those big alumnum stringer/floor supports.
I noticed one of those had an obvious bend to it, so I straightened it up and added some bracing.
Later I figured out that the hull wasn't true, so they bent that stringer to make the floor sit "flat" with the hull.
Then I could almost hear my grandpa say "You're building a boat not a piano!"