Hi Toni,
Circling back on your topic, I can share this short article about the artist Joseph Cornell, master of the shadow box medium:
http://www.ccaha.org/uploads/media_items/wonderland-preserving-the-art-of-joseph-cornell.original.pdf
The article discusses the context of Cornell’s shadow boxes, which informs how a conservator approached their treatment. You may consider this in regards to your collection and make your decision about preserving the shadow boxes based on the value of keeping the original configuration versus any detriment certain materials might pose to one another when in close contact. If you do decide to separate the elements it is of course important to document the process so the boxes could be easily reassembled. One suggestion is to treat the process like you would an album of clippings or photographs that required disassembling- taking pictures of the object beforehand and numbering everything based on its original location.
I hope this is helpful and I would be happy to find answers to more specific questions if you have them.
Best,
Maggie Wessling