Recurring Infection

Haven't posted here in a while.  We're still CD our toddler with flips and prefolds, and I can count on one hand how many disposables he's been in.  I came back to ask a question about stripping.

DS has an infantago (sp?) infection that started about 6 months ago.  We cleared it up twice, and it came back after a few weeks.  We've been running our diapers through the washer for 2 cycles, (cold rinse, hot wash w soap, cold rinse, cold rinse, hot wash w soap, cold rinse, cold rinse) but the infection keeps coming back.  This time around, he's on antibiotics as our pediatrician thinks the infection is too internal for cream, but I'm taking no chances and am switching him to disposables until it clears up.

In the meantime, I'm going to try stripping his diapers, especially since the flips I want to use on LO2 someday.  He's been in the same prefolds for over a year since he's so little for his age, and they're so ratty and threadbare that I don't mind tossing them if I have to.  He's so close to potty training that I don't want to buy a new set he may only be in for 6 months tops.  What's the best way to strip our diapers that won't hurt my flip covers?