I only remove the eggs that are clearly not developing, if I am not sure I leave them. Some people candle frequently, I am not sure if this is good for the embryos, since I have been using a very bright light (120 lumen LED flashlight) so I only take a quick peek once weekly. You notice there are all the dark welsummer eggs left, they are very hard to candle.
Any eggs I am not sure about I leave. Most eggs that are not developing will not go bad (rot), eggs are naturally resistant to infections unless the egg has been disrupted by cracking or pores that are too permeable; what usually happens is that is just sits there, and eventually does not hatch. You can take an egg and leave it at room temperature and it will gradually dry out until the contents are just solids, without it rotting; this takes a long time (in the months range depending on the humidity). Good science project! Bad eggs will smell bad, and if not removed explode (very nasty and smelly).