Hollo, they can definitely take swabs from the pustules if they are weeping liquid of any sort. My DD had these awful ulcerating mouth sores which were a complete mystery until the Dr took swabs and ten days later voila! it was actually from Chickenpox (she'd been vaccinated and it was one of those freaky things, mouth only).

If you are not happy with this Drs response, take your DD to another Dr for a second opinion (I did and the second opinion Dr was the one who took the swabs and solved the mystery). People do this all the time and it's quite acceptable to Drs to do so.

Re the school sores, yes I would think they could come back that quickly if a) they didn't heal completely last time or b) your DD has been in contact with someone else who has them (they are wildly infectious and are an excludable condition). I wouldn't worry about serious damage, if you have any questions certainly ask your Dr and I'm sure they will reassure you that all is ok. Let us know how you get on.