I just finished reading Justice League 3001 and it ends with a cliff hanger. Not surprising given the title of the issue is “Canceled”. But the series ended very close to the launch of Rebirth but does not give an indication of what series it might continue in.
From what I can tell with some Google searches, it seems that there is no proper ending for the 3001 storyline. I’ve read that the Rebirth Blue Beetle story does tie in very slightly, but then there was a writer change and there wasn’t much done with it. So, as of now, 3001 is just an unfinished story. Sorry if this isn’t much help.
That said, I’m not the omnipotent being of all DC comics lore so I could be missing something in my research. Hopefully someone else might be able to give you more info. I’ve got my fingers crossed for you.