holenailstrim
I removed some trim boards and I used the technique of pulling the nail through the wood to avoid splintering the finished face (instead of pounding the nails back out).
This resulted in the heads of the nails enlarging the holes slightly.
Since the oak is old, it is as hard as cast iron. Driving nails into it results in bent nails. I could predrill holes but that is extra work!
Are there any tricks to reuse the existing holes?
The key criteria for me is the size of the holes. If you used brads, then I have no problem with using caulk, especially on baseboards. The only possible downside is if you leave a fingerprint in it. You have to have eagle eyes to pick out a small hole like that.
With crown molding though, I'd plan on a lightweight spackle. Mostly because of the cost and effort you already put in installing it, might as well finish it nicely. Vinyl spackle works great, but again if the holes are small, just about anything made by DAP works fine. If you find yourself with a large hole, bondo (auto filler) does amazing things. Or you can use painter's putty, glazing, just about anything can be made to look really good. Sand and touch-up as needed.
Countersink with a nailset, struck with a hammer.
Fill with painters caulk.
Best Answer
Just two quick things.
Given that your nail heads were covered, I would have just bent them back and broke them off. But if they came out and you have holes on the other side that's fine. Honestly every trim/nail-type might have a best method so there isn't anything that someone can categorically say.
To go into existing holes... Get a better quality trim nail and use a gun. Up the pressure on the gun. When nailing into existing hole you want to hit the hole at an angle - maybe 30 degrees - so that your head doesn't shoot straight through.