Yeah, I was meaning something on the lines of that ^.^;
I'm guessing that anything that has had Lavos' energy added into it loses it's Red Dreamstone colour. This can give Magus' Amulet 2 options.
1) Magus' amulet is made out of dreamstone, charged and he was only hurt by the Masamune because he was around a gate that connected to Lavos (That means the Masamune should hurt Lavos cuz it is Dreamstone)
or
2) Magus' amulet is not Dreamstone but something like the Belthasar sealed door's that only open when Schala's pendant is used on it. (This works out because the Masamune is Dreamstone, if the amulet is something from the same metal as the sealed doors then the Masamune will have some kind of effect on it, or not)
Either way, my belief is that the amulet giving was pure drama to show how Schala knew that something bad was going to happen (black wind howling in that scene) so she decided to give him an amulet that would protect him.
BTW, what is the 2nd sword next to the thing that might be the masamune in your post Chrono'99?
Oh and on the note of Schala pendant, if it glows, i'd imagine it glowing red like in one of the Scenes with it. Maybe when it is used it's red, just like the scythe that Magus used against Lavos. It looked normal until it hit Lavos making it look red.