Unless you were getting measurable ammonia/nitrite, I personally wouldn't do a water change while there are eggs/fry in the nest. I'd probably be inclined to add a few drops of Prime to temporarily detoxify the ammonia, and then do a water change once the fry are free-swimming.
You don't want to disturb the male too much while he is guarding his nest. Some males won't care, but others may eat the eggs or abandon the nest.
I breed wilds so I'm a bit more gung-ho than the average Betta splendens breeder. However, I used to siphon out my grow-outs with a piece of airline tubing to avoid sucking up fry. Then I would slowly drip the water back into the tank using some more airline tubing to avoid shocking the fry with a sudden change in water temperature/pH.