I think the camera angles made it painfully obvious what was going on in that scene...
Starts with an establishing shot, putting us on the right side of the bridge well after the battle was won, then they specifically focus on the either Blanhaerz, or the abyss... There is an obvious focus on where we threw the eyes; It's entirely ambiguous, I really don't think we can out right say the eyes are gone for good... It could be a retrieval, or they could simply want to make sure we've lost the tool we used to slay the last Ascian, though the later seems kind of unlikely given we have Hraesvelgr and Midgardsormr at our side now, possibly even Tiamat...
I disagree with the notion that the eyes reentering the plot would make them the sole focus... We have no idea what Elidibus has in store for them, if he has anything planned for them at all... It's entirely possible that they could be used up entirely, rather than remain as they did with the Ascalon... There is also the possibility that we out right destroy them following their return, or seal them away properly... That was the plan, after all... Both Estiniens and Haldraths... Both wished to take them out of the reach of man and dragon both, and Nidhogg returned to get in the way of that... Now Nidhogg is gone-gone, and we have a scene ambiguously focusing on their new resting place... The possibility is there IMO...
And again, Yoshida mentioned that we'd find it less stupid that Estinien picked them up at the end of 3.0... Why? Nothing has made that seems any more or less stupid... All that's happened is we've thrown them away and the Warriors of Darkness are interested in that fact... At the very least, that implies we've made a bigger mistake than Estinien in casually throwing them away... Doesn't mean they'll be retrieved, but again, we have four, maybe six other eyes we can borrow to aether-blast Elidibus... I'm doubtful, after Hraesvelgr was convinced after Midgardsormr mentioned how he hopes this is a new foundation to battle the Darkness, and after Hraesvelgr already let us borrow his eye, that they'd deny us such a tool to battle the Warriors of Darkness... If Elidibus simply wanted to make sure we'd lost our aether-blasting balls, well... Might as well continue the XIV tradition of stupid antagonists, I guess... "They've lost Nidhoggs eyes after borrowing Hraesvelgrs! They have no more eyes to blast us with!", "What?! You borrowed Hraesvelgrs eye again?! Unpossible!", yeah... Lets avoid sending Elidibus out like that please...
That's to say nothing of Lahabrea, I'm not going to bother repeating that argument, everything that can be said on that has been said... I'll just continue to hope he returns because for some reason that line of speculation seems to annoy some people... I'd like a recurring villain we actually fight and who gets more and more twisted with every encounter and Lahabrea is the perfect candidate, we had our Seymour fight in Praetorium, then he came back as Ascian Prime for a Seymour Natus, now I'm waiting for him to rise out of that abyss for a Seymour Flux battle...