I take out the chicks to change the nesting material. However I don't handle the eggs, unless it is really important.
Try adding/changing the wood shavings without disturbing the eggs. Once all eggs hatch, you can clean/wash/replace the concave as well.
Keep the wood shavings open in the room for few hours before placing in the nest box, if there are eggs.
The hens' incubation is different after the chicks hatch as they feed the chicks as well. So she will be feeding as well as incubating. So let her do that. If she feels that the eggs are not going to hatch, she will remove/corner them and won't incubate at all.
Handle the babies twice a day for 15 to 20 minutes, once they are 12 days old or so, hence they will be tame. I always wash hands before handling smaller chicks or wear disposable gloves.
I sometimes clean a nest out even if it has eggs still in it. Clean your hands first then carefully take the chicks and eggs out of the nest, then change the shavings.
It is up to you if you handle the chicks or not. If you want hand tamed chicks I would handle them. I wait until the chicks are two weeks old before I take them out of the nest once a day for about ten minutes at first. As they get older I take them out for about 30 minutes at a time.
As for the coloring of the chicks if you are colony breeding you can never be sure what color the chicks will be. Even if only the two birds you are talking about bred we would need a clean photo of both the front and back of the birds to tell the mutations.
The male looks like a sky blue, yellow face type two, opaline, grey or clearwing. I can't tell the mutation of the female. Are her eyes red or black? If her eyes are red that means she is lutino if they are black she could be a dark eyed clean, double factor dominant pied or double factor spangle.