Mmmkay, I recently watched both versions of that scene, and it looks like it could be the pendant... But how did the pendant appear by the other party members? I noticed that after the members were warped out the pendant still remained on the floor. Now I know Logic usually isn't followed in videogames, but how the heck is an inanimate object supposed to get out of the deepest chamber, of an underwater base, and know exactly where the party members are so as to find them ALL before they were found?
A thought I had, that is a major stretch, is that the sparkle is possibly a piece of the time egg. We see the egg shatter, and that is the last we see of it. Im thinking that maybe the shattering of the egg sends the little shards travelling through time. One of the shards finds crono landing in his shirt. Once it does it flies up and brings the party to the scene. The body is then replaced and they leave. The time egg piece falls to the ground, and is set to rest on the Black Omen.
However this still leaves a plot hole. How did the pendant find the party? I'm thinking that when Chrono was destroyed, The necklace remained in tact, possibly from being infused with Lavos' power as other's have suggested, and blew onto one of the characters. when they were teleported out, the Pendant fell to the ground, and was later found by a villager.
As I said it is a bit of a stretch, but I also think that would explain Crono's amazed look at the tiny little sparkle. Also, how would the Pendant have gotten disconected from Crono's neck to float into the air and astonish Crono?