You know what was told: that some relatives took advantage of the last days of Queen Amelia, since HM was not always 100% lucid. I do not know if this is truth but as we say in portuguese 'onde ha fumo, há fogo' ('where there is smoke, there is also fire', in a free and very literal translation). But we must not forget that Queen Amelia was robbed at least two times: one when she was travelling and another in the Chateau where HM lived.
About the sapphires, I think there are much more jewels (possibly sapphires) in the Braganza vaults but clearly D.Isabel already has her favourite pieces and it will be difficult to see 'new' major jewels.