There are a couple of schools of thought. Both of them involve tapering the holes.
Some people taper the holes and fill with a fiberglass reinforced short strand filler.
Some people taper and fill with a slurry of chopped fiberglass matt and resin.
I personally like the resin method. Applied properly you will need minimal if any filler.
For tapering the hole I have used a little 2" rotoloc disc, enlarging the overall size of the hole to about 1". I have also used a 4"grinder and made the hole more elongated in appearance. Both have worked.
The key is the taper. Don't worry about making them larger.
If you wondering if you can just fill them as is....then the answer is no. They will spot through or crack.
I know its a big job....but this is really the only way to do it.
This is the method I used here: