I asked around for more advice on your situation and received this informative response from Mark Nesbitt, Research Leader in Economic Botany at Kew Gardens:
“It’s true that there is potential for substances in the packaging to damage the contents – and vice versa.
That said, I would look to see if actual evidence of damage is present. In some cases there might be e.g. foil barriers that prevent this (I’m thinking of the foil-lined cigarette packets of my youth). There is a delicate balance between preserving the integrity of the object, and preventing damage, so each item should be assessed separately.
In cases where discoloration etc is taking place, then yes I would take out the contents. I would put the contents into a conservation grade transparent plastic container. Then I would take a single container, put in a layer of Plastazote, and cut two spaces, one for the box of contents, and one for the original packaging. That way, both are preserved and both are stored as one object.”
I hope that helps.