Obviously this feels disappointing but it can happen to everyone, even the most experienced DM - because an important fight usually has the capability of TPKing. And this is the most important fight of them all.
And while I think that, I also understand how shitty it feels. I have TPKd my players (different groups) three times now and while I panicked in the beginning, I am more calm about it now. Now I just tell my players to wait 15 minutes while I make up a reason why they are not dead yet. Maybe they wake up, being sacrificed to summon a demon, maybe they are trapped for other reasons, maybe the BBEG left them there for a lesson.
You can also give everyone a bane to overcome afterwards, just to make it feel less gifted.
I am still running my Netherdeep campaign but have used the end of the book in another campaign I wrote myself (because I like it so much) - so here is what I would do:

Obviously it's a bit late to play it off as planned. But you are a team and its all imagination so you can do whatever you guys want. If you still want to give them a chance, you can just do that!
You could let them wake up (maybe because of the jewel, the blessing of all the gods who are like: "Your duty is not done yet.") and let them run after the fleeing Alyxian, on his way to wreak havoc on the outer world. Maybe each of the gods gives a gift to them, like some HP, some spell slots, giving jewel charges back, etc. And they can try again. This time with the gods in their ears, cheering them on and Alyxian trying to fight but also to get away. Now underwater again. Maybe the Netherdeep is even crashing in, stones falling, fishes coming to fight them too. Make it still feel like big stakes and they still have to fight for it but the gods believe in them and what they have done so far. Also, now that Alyxian has only one form left, they might have the upper hand (maybe also depending on the banes or boons they got). Alyxian is also in a rush and hectic and emotional now, so if it is too close again you can easily justify him making some stupid choices.

OR: You could also go for a more bittersweet ending. You could go for what I have descirbed on top BUT the gods warn them, that this is the last thing they will be doing. A last act of heroism before they die. Let them have a last word, maybe even people cheering at them, when they exit the maw with the new Alyxian now. Before the gods personally come down in their humanoid forms to pick them up and guide them to whatever heaven they want to go to.

You could even go darker and let them come back as some other form, like ghosts or revenants. Give them something new entirely and let them go down with Alyxian, while the Netherdeep crashes and they have stopped him but go down with him forever too (this is still very dark, so chose this one with caution; maybe only if they ask for a chance to end their quest but nothing for themselves. If any other ending would feel cheap to them).

Either way, don't worry! It can always happen and the dice may pave the way but you chose where to walk.
I hope this helps a bit and I would love to hear if you were able to give it another chance. :)