Adding my 2 cents/experience…
I run a private server and this issue has come up a bit recently, so I did some testing.
Note: server settings are default/mirror official. Vault refresh mean is 105 minutes with standard deviation of 30 minutes.
I ran 3 different vault, cleared everything, came back 2 hours later, as MY experience over on Official PvP was that the sigil chest at the end was on a separate timer from the vault reset timer. The box on each vault I ran reset. So I did this test again, waited 2 hours, and went back. Again, the box on each vault reset.
My experience was that the sigil box at the end was on its own timer separate from the vault, just like the legendary weapon boxes are, and so far, this experience is playing out to be correct after doing a few trials.
I wonder if any other admins are able to replicate this experience? For what it’s worth, I think most people are assuming (and the assumption makes sense), that the sigil box is supposed to reset with the vault, when in fact, it does not.
My comments only pertain to the sigil box and legendary weapons boxes. I have not tested any of the other boxes out in the open world that people have reported as not working.