Well, you already said what I was going to say about the magnificent sapphire collier de chien. It is an interesting exercise to think who should had inherited it: that is the same to ask if that jewel should be considered portuguese or french. I mean, it was purchased with portuguese or french money? Personally I think it should be considered a portuguese jewel, since when it was purchased probably when D.Amelia was already Queen. Hence this choker should have been inherited, imo, by D.Duarte.
About the pearls, I have no doubts: they should have been in the Braganza vaults.
In the 2nd picture of Queen Amelia that Cristina posted you can see a large brooch in the form of fleur de lys. If it is the brooch that I think it is, it was a wedding present from the Rochefoucauld family (close friends of the Orleans family). It was made with diamonds and ceylon sapphires and was a favourite jewels of Queen Amelia that always proudly wore it. whereabouts is unknown to me
In the same picture you can also see two small brooches that probably were made of diamonds and sapphires. The provenance and whereabouts is unckown to me.