The new movie is set six years after the huge point of divergence introduced by the Borg attacks of 2380-2381. In Needs of the Many, Janeway says that the unusual characteristics of the Hobus supernova (a star light-years away vapourizing a planet so soon after it goes?) makes it a likely candidate for artificial supernova, probably as a side-effect of the subspace weapons tests made by Sela's faction but maybe by Species 8472. In a timeline that's had at least six years to diverge hugely, it's very possible that those weapons tests wouldn't have been made, Hobus would remain intact, and Romulus and Remus would have survived.
You need to think about this more metatextually. The "timeline split" is merely a way to rationalize the fact that Pocket Books and the makers of Star Trek Online
have chosen to develop the post-NEM continuity in different ways. But all
licensed tie-ins are required to conform to screen canon, even when they don't conform to each other's continuity. The destruction of Romulus is screen canon, and therefore Pocket will be obligated to include it in the novel continuity, even if the specifics of its inclusion differ from what STO established. Real-life contractual obligations trump fictitious continuity rationalizations.