Yes, you are absolutely correct  Budgies lay a set number of eggs in any given clutch/cycle regardless of how many eggs they have under them, unlike some other species such as canaries who will lay a set number of eggs and will replace them if they are removed.

Removing an infertile egg will not cause a budgie to lay another egg, and I prefer to leave infertile eggs in a clutch with fertile ones to provide support to chicks that hatch, as well as additional heat to the little chicks when momma leaves the nestbox  

Eggs that are fertile will slowly start to darken in color as they develop, rather than being more opaque in color when they are mostly full of fluids to begin with. 

A picture if the eggs with a light shining though them would be the most easy way to see if they are actually fertile or not at an early stage. If you wash your hands thoroughly with a natural soap, there really is no problem at all with handling them quickly while doing this in my experience 





The only way you can damage the air sack is with a harsh or quick movement. Momma rotates the eggs routinely to prevent them from sticking to any side of the egg, so movement itself when gentle is not a bad thing 

I would wait a bit longer before righting off these little ones. The most common to be infertile are the first and last eggs, so the middle ones might still very well be fertile after a few more days