Glad to hear that she's finally digging again!
You asked..."Does she usually lay all the eggs at once? Or does she do it multiple times? and if it is multiple times, do I need to wait until she's completely done before I dig up the eggs or can I dig them up between her laying times?"...she is supposed to lay them all at once. Let her lay them and bury them completely and let her go back up in her branches...then dig them up.
Water and feed the chameleon well (dusted, gutloaded insects) for the next few days and then cut the amount you feed her back to normal.
Have the container that you plan on incubating them in ready first. I use a shoebox sized tupperware type container. I punch a couple of tiny hole in the lid. I fill the container about half of slightly moist vermiculite (dry enough that you can only squeeze a drop of water out of it). I fill it only half full so that when the babies hatch they have room to move around until they can be removed from the container. Once you put the eggs in the container, put the lid on it and put it in the incubator.
I dig the eggs up carefully by taking off one layer of sand/soil at a time until I reach the eggs. I carefully lift one egg out at a time trying not to turn/rotate them when I'm doing it. I lay the eggs in rows about 1" apart in all directions in a slight depression in the vermiculite. By spacing them this way they will hatch more individually and I have had a better success rate and survival rate doing it this way. Put the lid back on and incubate them.
Since I have never incubated flap eggs, I can't tell you a definite temperature....look in the sites that I gave you before and see what they say. You're better to err on the side of lower than too high.
My fingers are crossed for the successful laying and hatching of them!