Someone have been working on this one for a while now and he think's that he had tested it enough to finally confirm it. So remember the first phase of the VoG when you need to defend the sync plates? And after you complete it there's that little song that plays as the spire beam is opening the door? Well there are three different songs that can play there and he figured out what triggers each one.
The song is at 2:09.
The second song will play on hard difficulty if you lose a sync plate during the phase. You'll know you've lost a plate when the message pops up saying, “The Vex are taking control of a Sync Plate”. Here is a video of me completing the phase this way, triggering the second completion song:
The song is at 4:48. It’s kinda hard to hear over the shotgun but he included some links to cleaner videos of each song at the end.
The third and final song, the one that he believe is the “correct” song to play, will only play on hard difficulty if you complete the entire phase without losing a single sync plate. Here are a couple of videos of me triggering this song:
The song is at 3:21.
He tested each song multiple times to make sure that that's what triggers each one and that they aren't just RNG. This pretty much confirms that there is still some sort of secret left in the Vault of Glass.
The next trigger might be somewhere in the Templar room since another song plays when you kill the Templar but he have no idea how to get it to change or if that's even what will change if that part of the raid is done correctly. The Templar song is the same whether he is killed on normal, hard, or with no teleports on either difficulty so maybe there is something that needs to be done during the conflux or oracle phases, or maybe there's a Templar trigger besides no teleports.
Also, as a side note, one of the Cryptarch’s pieces of idle dialogue says, “Now what use would creatures like that have for music? No... It's language. Code, signal!”, so maybe the songs have some deeper meaning if we translate them somehow? Anyways this will hopefully get us on the right track and get more people interested in finding the secret. Everyone should keep in mind when searching for secrets in the Vault that they might not find anything if they haven't done everything right up to that point.
For reference here are videos containing just the songs.
Hard mode, plates lost:
Hard mode, plates kept:
Doing the spire phase of VoG without losing any sync plates makes a different victory song play.
Note: A good point brought up by u/doughnut_cake: I don't think that the next phase of the puzzle is as simple as completing part of the raid without sacrifices/marks/teleports. If I had to guess I would say that the only reason the sync plate thing was so simple was to get everyone on the right track.
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Credits: Special thanks to jessej37 for sharing his thoughts about a possible new secret in Vault of Glass.