We don’t know really what happened to the red slippers.
From The Doctor…
Rumpelstiltskin: What about the slippers?
Jefferson: Oh. Couldn’t find ‘em. Heard talk they’ve already been moved to another land.
Rumpelstiltskin: That’s what I needed to get to that other land.
The slippers are in our world, with Dorothy.
Not everything went to SB, there was Snow’s cabinet etc so there is still stuff there at Rumbles place.
A crystal ball isn’t just some random object. I’d imagine that Rumple saw to it that all of his magical valuables ended up with him in SB.
As for the necklace that Emma through down I don’t recall Bae ever picking it up and why would he keep it at that time he loved Tamara.
Neal has always been in love with Emma. Whatever he did or didn’t feel for Tamara, he NEVER fell out of love with Emma, and I simply cannot imagine that he would have left such a specious momento sitting on some bar.