Well if one of them is permanently dead or absent or whatever, it's probably Solas (sorry guys) because... well, I just can't see them doing 3 games' worth of buildup about What Is Flemeth Up To only to unceremoniously remove her from the plot like that.
Well, they did reveal what Flemeth was in the end after that build up. She has a big role as an NPC, true, but also is pretty absent save for a handful of scenes through the trilogy. Still, I see your point. Solas himself is a new character, while Flemeth has been a poster child for Dragon Age next to Morrigan since the beginning.
I also can't imagine Flemeth willingly turning into a dude. Doesn't seem her style what with all that "eternally wronged by men" stuff and only having daughters to live on through.
(Also is it just me or did anyone else think Flemeth conspiracy theory when they read that codex entry about Andraste's descendants all being women? WHAT IF ANDRASTE IS FLEMETH OMG o.o)
I think it would be pretty cool if Flemeth was Andraste with Mythal's spirit after Maferath's betrayal. The story of Conobar and the bard could very well be allegory for Maferath and the Maker. That's a lot of religious figures all wrapped up in one (especially when you throw in Fen'Harel into this deity cocktail), but I find the implications interesting. We've had confirmations of some truths of the elven pantheon, but not so much the Andrastian faith. It'd be nice if they overlapped some.
Flemeth can be dead and yet still come back. We can kill her in Origins, yet there she is. Morrigan says she can't really be killed (probably).
I think Solas is borrowing her god mojo for a while because he lost his, and later she can transfer again if needed. The elves apparently did this- think of the soul gem in the Arcane Warrior quest. He got trapped there because there was no one left who could help him leave.
This is a good point, too. It's already established that Flemeth is damn near impossible to kill (if it's even possible at all).
"Shall you slay the old wretch as the legend goes, or will the tale go a different turn... It is a tale poor Flemeth knows all too well."