1.0 relics carried over and they built upon them so I don't see why they wouldn't again. What could happen is them simplifying and unifying the entire quests again, like they simplified the 1.0 relic quest, and make a single questline that gives you up to Nexus, and then work from there up to Zodiac with nerfed costs and what not. Though they could also just make a single questline that gives a fully upgraded i135 or whatever Zodiac, and once again work from there to whatever the next weapon forging quest will be.
Of course it would screw over everyone who worked for almost two years on their relic, but they already kind of did that in ARR with all the people who spent months in Hamlet and millions in crafting and melds, so they might do it again. Like the 1.0-ARR relic quest carry over, it most likely will also account for whatever progress was made, but of course with varying degrees of progression and more or less regret depending on which step you were at.
Just like doing all those Hamlets and spending all those millions put you up to Hydra, but if you didn't even get to the unfinished relic step you were left with an ok, but ultimately useless for the relic questline, weapon that was also already outdated since it was worse than the Moogle weapon you probably already had, and then you still had to do pretty much everything else from the start.
