Aaagh, that makes me want to stop playing until they fix it since I just finished my third playthrough completely and started focusing on the fourth. I wouldn't want to miss out on a bunch of amulets if I can help it.
My main (and really only) playthrough is more or less paused until this gets sorted. I likely won't have any other real playthroughs this year, so I want it to be as complete as possible, but I was just getting to a part that blocks progress (since I can't return to the Winter Palace, a later fix for Vivienne's amulet there wouldn't help at all if I continued) before they went and messed it up.
BioWare hasn't chosen to comment on the situation, so it's anyone's guess what's going on (they are aware of it, though—an EA agent remarked twice when it was brought up on the support forums, so it will have been passed along). Like I said, it's possible they moved the amulets, but nobody has really found any new ones yet. I don't think they were purposely removed altogether, as again that would leave Dorian with no amulets, for instance, while somebody like Blackwall still has at least 3.
It seems that the only amulets left in containers are ones where BioWare could remove all the other treasure (Cassandra's amulet in the Fallow Mire used to have some Chantry-related valuables with it, but it's the only thing in the chest now). If there was unique treasure in addition to the amulet, the amulet is gone instead (it doesn't even matter if it was something that could be exploited or not).
Hopefully we'll at least get word on what the expected behavior is by the time Patch 6 releases next month. At this point, I wouldn't expect any sort of fix before then.