Re: Prepping to re-bed stanchions.
I would pot the holes if you have any signs of water intrusion. Removing that first few mm of wood will let you know if there is water in the core.
If there is water in the core then you are onto a much bigger project, and one that I have no personal experience with. From reading a lot of threads it looks like the core will not dry out on it's own. Potting a wet core with epoxy can just trap the moisture, not eliminate it. It depends on how bad the situation is.
Epoxy is easy to deal with. I rebedded my stanchions one or two at a time on down days while cruising and didn't want to mess with it. If I were doing things again and back at my slip I'd pot them.
boats that I sail on regularly: Pearson 28-2, Rondar 505, Yankee 30, Blanchard Junior