I do wonder if Luke's crystal will be addressed at some point in the new canon. Could be Qui-Gons, though I though Obi-wan gave that to Anakin before Anakin made his own.
Is that from any of the new material, or from an old EU story? Either way, it's possible Anakin gave it back to Obi Wan after he built his own.
There is also a slim chance that Luke's green crystal was Ezra's from Rebel's Season Three (why Ezra's new saber is now green is unclear since his first once was blue, and the crystal might have survived).
Ezra's crystal did indeed survive the hilt being destroyed as it was clearly visible amidst the debris. Whether he grabbed it before going after the holocron is as yet an open question, though it would be the simplest explanation since another trip to the Lothal temple is obviously out of the question.
Not sure how or why a crystal would change from blue to green though. A sign of his changed nature perhaps? But then why did Anakin/Vader's saber remain blue? Perhaps the change is something only happens when the saber and crystal are first constructed.
For a second I wondered if Ezra pocketed the ancient Jedi cross-hilt he picked up (which was green bladed), but looking at the scene he sets it down on the ground right before the Inquisitor shows up. If he grabbed it again later, we certainly didn't see it.
I can guess that Anakin managed to pocket his original crystal after his first saber was chopped on Geonosis. Though it wouldn't be out of line to fine a new one. I expect Obi-wan had to do the same since I don't think they ever recovered either of his earlier lightsabers (the one kicked by Maul on Naboo, and then one taken by the Seperatists at Geonosis). Though there would have been a surplus of lightsabers in the arena following the battle with over 150 Jedi dead on Geonosis.
Clearly the Jedi do keep a hold of spares as both Obi Wan & Anakin were thrown a hilt during the arena rescue. However, I would suppose that if a Jedi is to have a blade that's truly an extension of their body and will, then they'd probably either go back to Iilum or do as Ahsoka did and "reforge" (for lack of a better term) an old crystal in a new hilt.
Ahsoka did mention in the novel that she had previously visited Iilum three times. Once during her "Gathering" ritual as a youngling and again as a padawan when she chose to make herself a second blade and of course as we saw the third time when she escorting the younglings with Yoda.
Anakin's old crystal calling out to Rey might be interesting, as the Crystal(s) are declaring its her saber, or it things she is the best way to get back into a hand of Luke's. Still over a year before we get something like a clear answer on that one.
The way I'd choose to interpret it is that Anakin's old crystal isn't calling out to her in the sense of a thinking thing, but rather resonating to her presence. It "knows" he because the force transcends time. The crystal itself is just a conduit and a mirror.
It's functioning sort of like an un-collapsed wave-function, showing her one possible future. It's also probably no coincidence that it cried out to her in her own voice as a child. Self-reflection is a recurring theme with force visions and insights.
