Actually, according to
@MonsterEnvy they both barely survive in the module:
So it looks like per the original adventures
@Uni-the-Unicorn! was correct in think Ember and Verminaard should be tackled separately.
The point I was making in my original reply was a simple one: w
hat people recall about DragonLance is overwhelmed by their recollection from the novels, not the modules. That is "everything wrong about DragonLance in two sentences".
As for the narrative hand-waving of what happened to Verminaard offscreen - all of that occurs off-screen. The PCs have no real way of knowing what occurred. Flamestrike is just a Maguffin NPC to provide the PCs with plot armor at the end of DL2 as to why they don't get incinerated by a massive red dragon.
The final confrontation with Verminaard in DL4 -- (if inded it is final, even then it is left as an obscure death) -- is up to the DM to determine. Yes, Vermi and Ember together are overwhelmingly powerful and will wipe out a group of 7th level adventurers; that was my initial point above.
Anyways, look -- I'm all for reviving the Classic DL Campaign and running it in 5e for players who have their own PCs, and in a manner which is open enough so that the turns and twists the path of the AP takes are in the hands of the players and the DM -- and not in the hands of a pair of novel writers or module designers. There is a LOT that is good and
great about DragonLance and its larger narrative tale. It added immeasurably to gaming and D&D and that heritage lives on to this very day. It's just that the novels left such an indelible impression (especially
Dragons of Autumn Twilight) that it's really hard to free your mind of the mental chains the novels create. It's not simply
necessary to break those chains -- I would argue that it is
vital.
In the end, those mental chains are the REAL BBEG in any Classic DL campaign. Win that fight? You win a great campaign for you and your players.
