As you said, too early to get a clear picture. The story doesn't really explain the extent of this development and the effects it might have on other characters outside the Superman Family. Still, a new designation seems too far a stretch, since the characters just regained all of their NE backstory. It wouldn't be right to make new pages for them, yet.
It is still troubling that somehow, PE has been merged with stuff from NE, but we can't really point out what to do next. The logical thing to do is to wait for the developments/aftermath of this event, which will likely happen in Action 977 and furthermore in Batman/Flash: The Button special. As soon as we find a solid answer to what the hell is DC doing now, we'll throw ideas to work around. Until then....
At the moment, if you want my opinion based on only what I read from that article, I would say we go back to the New 52 Kal-El (Prime Earth) page for the sake of keeping the designation consistent, acknowledge his death and their combination together, while also giving the old memories their own section right after his origin called "Post-Crisis Adventures" or "Early Adventures" or something like that.
Again, take this with a grain of salt. No body knows where this development could lead us but, when we get a better idea like S said, we'll discuss what's the best course of action. (And I'm sure the other admins will each have their own solutions to suggest as well.)
And after a second reading of Action 976, it seems that all the incidental dialogue of the issue was written to illustrate that PE, and all New 52 characters were somehow split in two in Flashpoint. Meaning that this merging is simply an official return to Pre-Flashpoint stuff.
That said, the best bet is still to wait, but I can already see the indexing mess this whole affair will bring.