Your photos clearly show--your dolls are giving off or reacting with some sort of destructive chemical possibly in the paper, or the doll itself. Leaving your dolls/clothes in boxes, closed up---inside totes, with more plastics, or more unknown content cardboard/paper simply exposes them to trapped air-borne chemicals inside an already closed environment.

Storing dolls or items in acid free, archival materials would be recommended, just as you would keep antique books/magazines, prints. Museums are environmentally controlled with air purifiers, air circulators, and everything is carefully stored or displayed with safe lighting and safe materials around them. We kept the vault open in the University Library where I worked at least 4 hours every day---to air out the antique books stored there.

If it is the bodies themselves that are deteriorating, naked and out of the box with air around them might be the only solution.