I have 2 different proof commemoratives that the airtites have 1, cracked and the other won't stay closed. Is it OK to replace the airtites without affecting the value of the sets?
Of course - but you won't be able to buy the exact same ones and the replacements won't fit in the hole of the original box. The US Mint uses a different manufacturer for their coin holders - they are not Air-Tites - thus the different size.
