I honestly wouldn't suggest removing your snake from her eggs at all, unless you intend to artificially incubate. I have never seen my female more upset with me than when I removed her to count her eggs. And I have never seen her more psychologically distraught than when I did that. Her immediate reaction was to keep moving toward the tub, dodge my hand and hiss, and keep moving toward the tub. I felt horrible.
Pretty much everything that happens she will try and get back to her clutch. If you are going to feed, as said before just offer her food while she is on the clutch. Personally I will continue to maternally incubate, won't offer them food while they do so, and will remove them only once to count the eggs. Additionally during the pre-lay shed I will remove all bedding and put in fresh bedding, then not even bother to clean it more than spot-cleaning, if necessary. I loved maternal incubation, but I am going to mess with the snake as little as possible unless absolutely necessary. My own curiosity cost her a baby (she reacted and I'm sure that is what broke its neck), and honestly I would hate to ever remove the snake's eggs because of the stress generated by counting, and removal to finish incubation artificially.