Thank you, Dai and Sunnie! Still I'm not sure if it means that there are several Flemhorcruxes around, but it's certainly intriguing. I do hope that this is not the last we've seen of Flemeth, she's my favourite character, but as everything with her what will happen it's anyone's guess.
@Dai Since I learned that the Ultimate Sacrifice is canon for Bioware, I don't like to include speculations about the old gold soul in the main story. I think that Flemeth simply knows that Morrigan will find the grimoire and convince the Warden to kill her. A lot of Flemeth's actions, the ones we seem in game at least, seem to be about testing Morrigan; that's why I think she will be the one to play a similar role if Flemeth is gone. I'm curious to know whether Bioware said who drinks from the Well of Sorrows in their canon; if it's Morrigan, I'll say that was Flemeth's mission for her in Inquisition.
I also doubt that there are other amulets or incarnations of Flemeth out there beyond maybe one. We don't know how the amulet works. That could have been a one shot that required a great deal of effort and magic to produce. But I am sure that the one we saw in the game and the one Solas met with was a "clone" of some sort, like the one we can fight in Origins. I also believe that in the case of an old god soul, Flemeth went from Kieran to wherever she was going with the soul. She did this immediately. She wasn't about to wait around with it and wait for Solas to show up. So she had done something with it before the post-credits scene.
As for the reason Flemeth left a clone behind while she traveled with Hawke in the amulet, I guess I can see it being about Morrigan killing her over the info found in the grimoire, but I just don't think that's likely. Yes, Flemeth can see into the future somewhat, but I don't think she could have predicted that the Warden would find the Black Grimoire in Irving's things, give it to Morrigan, and that she would act so drastically. I think it would have more to do with the old god soul, it's just that Morrigan didn't want to mention that as the reason. On the other hand, Morrigan did genuinely believe Flemeth was out to possess her body, and this was indeed true, even if Morrigan didn't have the whole picture.
I am certain that Flemeth is still alive. The scene with Solas shows her blue energy essence traveling into the eluvian. And the temple shows a blue spirit of a female (who is supposed to be an elf) rising out of the well and going into the eluvian. So I think these are connected.
Also, Flemeth is surprised if Morrigan drinks from the Well. So I don't think that was her intention for her, though she did raise all her daughters to want to preserve ancient magic. But this is probably because she wants them to agree to carry Mythal's will, as well as Flemeth's spirit within them.