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Normally they don't retain food for weeks, no. As long as they have access to proper temperatures for digestion, the majority of the ways clears their digestive tract in a matter of days. That said, I am not sure how her parasitic issues might affect her digestion. The meds also change the gut flora.
Pinky mice do have bones, even though they aren't as fully calcified as older mice. I wouldn't worry too much about unusual waste at this point unless it's diarrhea. If you're concerned, a call to her vet will probably help.
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