I had my own idea that was slightly more metafictional. Basically since Jor-El was already a temporal paradox, him taking Jon outside normal spacetime and returning him to Earth-0 as a teenager created a temporal "knot" that threatens the integrity of the timeline. The Time Masters (led by Rip Hunter) warn that Teen Jon is an aberration whose continued presence causes further damage, causing entire eras to bleed into each other. One of the major casualties is the Bendis Legion, whose timeline unravels as a result of the temporal instability because Teen Jon's presence is unnatural. Of course, this was all orchestrated by Dominus (a reality-warping villain from the late Triangle era) who manipulated events to both damage Superman's legacy and use the instability reshape the Earth-0 universe to his liking.
The only solution is to bring back Kid Jon to his proper place in the timeline and thus negate Teen Jon's existence.
Of course, Teen Jon resists anyway he can. Trying to find solutions that inevitably fail--reflecting how he was unable to rally the heroes in Dark Crisis and how Waller used him as a weapon. Eventually, Jon comes to terms with how his years-long imprisonment messed him up emotionally and made him fear that he'd become like Ultraman. Eventually, he gets some proper closure with Jay and makes the decision to go back to the moment Ultraman imprisoned him in the volcano, rescue his younger self, and restore him his correct place in the timeline. DC can frame it as a selfless sacrifice while restoring Kid Jon back to factory settings. It's not so much an erasure as Teen Jon still existed, but before his proper time so he could be bisexual in the future, but that's no longer the focus of his identity.