I think that when you disassemble a piece of armor or a weapon, you should get your ornament back, instead of getting nothing for it. This is more so for armor than it is for weapons, due to the fact that exotic perks stay the same. However, say you get a flawless vigil ornament and use it on what at that time is your best piece of trials armor, but then you get an even better piece of armor for that slot? Well at the moment you can't do much about that except try for another flawless attempt or your kinda just s.o.l. I don't think it would harm the game to receive refunded ornaments for breaking down your items, if not for the weapons...at least for the armor.
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I infused my arm piece that had in ornament and didn't even realize it right away. and its the only ornament i've ever gotten too. I don't know if contacting bungie about it would help get it back or not.