I had something similar happen with the Armadillidium I gathered. Seemed like all the adults I gathered died off, but then waves of their offspring matured and multiplied. I think they were just at the end of the their lifecycle, were unhealthy to begin with, didn't adapt to changes I put them through, or some bacteria bloom or slightly lethal chemical in the coco fiber or box slowly got to them before gassing off.
I only have several months experience with A. vulgare, P. scaber, Porcellio dilatatus, but I've had all of those cultures go through relatively damp and drier conditions without denting their populations as long as there was some moisture somewhere in the box. I don't have problems with phorid flies, I think because I try to keep springtails in all those cultures, which cover carcasses such that I doubt a fly could land there. My Porcellio dilatatus culture is pretty much wall-to-wall springtails, which might annoy the isopods a little, but they plow right through them and are reproducing anyway. On the other hand, P. scaber seems to have overwhelmed their springtails such that I can't find any in their culture.
Now, in all their cultures I always keep a lid with water and charcoal (to climb) so they have a backup source of hydration. I also use that dish as a visual gauge of when I need to rehydrate an area of the enclosure.