Speculation on my part but I think all larger pieces were brought into the foundation ensuring access to it.
The diamond and sapphire earrings Maxima wore for the investiture were as far as I know the set Queen Juliana had made from her mother's wedding gift parure for Princess Margriet.
Beatrix received the Bandeau a la Grecque from her parents for her 18th birthday and that also seems to be part of the foundation and has not been worn by it's former owner in decades.
The earrings Irene wore with the ruby peacock parure were never originally part of it. Wilhelmina and Emma did not wear earrings so had sets without them. Juliana had several made for existing sets. Wilhelmina did own a pair of diamond earrings part of the necklace/tiara she got from her father for her 9th birthday.