Even with the different age, it's the same character. They aren't erasing BM, and making Robin the one true hero Gotham ever had (this is like the Supergirl is now Superman thing sounds).
I can't see it a satisfying conclusion if you'll left your audience debating which character still exists.I disagree. Not only is the point of the conflict in the film less to do with Zod or Kara, it's solved via Barry finishing an arc and identifying the real problem. The rest? That's more so left in a general "everything worked out, but we nod that this world is very different". This is why it's treated as a shock when we see Keaton, Kara, and the Wonder Woman sign on the bus. This film's conclusion is now satisfied, and what's left is the playground they've made to explore in other films.
To be honest, they are making this shit on the fly, and without the Supergirl script being done or filmed, they can't address anything related to her character or the SM mythos, because they have no clue of what they'll end up with.