I try to explain it:
As far as I remember there are different Version of FUTURE CONNER:
1. Titans of Tomorrow Conner I:
This Conner was as far as I remember the original Conner who turned evil....(this was as Conner and Cassie had a date, they then went in to the future to help the Legion)
They met then the Titans of the Future for the first time....
Here Conner had Lex as new "Mentor" and called him Pa-he was married OR in a really serious relationship with Cassie, because Lex talked that he wants that Cassie and Conner get a child....
2. Titans of Tomorrow Conner II
This is the second Time the Titans of Tomorrow appeared (it was as Conner fought against Supergirl)...This was a clone created by Tim and Luthor...I think this is a timeline where Bart and Conner died, but DIDNT come back....because Conner and Bart were both cloned by Tim and Luthor...
Here Conner and Bart were evil....
In this timeline I think this happened:
Cassie and Tim were in a relationship, but then as far as I understood then Conner and Bart were cloned and Cassie was again together with Conner or so....
Because at the end Present Cassie kisses Present Tim and Future Conner want to kill present Tim because it enraged him, but future Tim killed future Conner, because if Future Conner would have killed Present Tim there timeline would have been erased...
3. Rebirth Titans of Tomorrow
Nobody knows, because they acted neutral and had only a short appearance...
BUT there is also
4. Kon El (Batman in Betlehem)
https://dc.fandom.com/wiki/Kon-El_(Batman_in_Bethlehem)
I think this is elseworld...
BUT!!!!!!!!!
Its also important to say, that this are all FUTURES OF PRE-FLASHPOINT!!!!!!!!!!
So I think that Titans of Tomorrow might show a future where Flashpoint,NEW52 and REBIRTH DIDNT!!! happen...
Because Titans of Tomorrow Tim asked present Tim about Conner and present Tim didnt know who Conner is...
So it could be that Titans of Tomorrow are completely seperated from the actual Timeline...