It's too early to answer that before it happens. It depends on the specific situation. Remember, we already had a new series on the air simultaneous with the novelverse, namely Enterprise. It established some things that conflicted with things the novel continuity had established (e.g. Andoria as an icy moon of a Jovian, or Tholians looking different from the scorpionlike appearance described in The Sundered), and later novels just tweaked those details to fit the new continuity, either finding ways to reconcile them or just glossing over what past novels had asserted. Heck, the Star Wars EU did much the same thing while the prequel films and The Clone Wars were coming out.
If a new series overlapped the same time frame directly, or if some obvious, massive contradiction came up early on, then yeah, we'd probably have to reboot the novel continuity. But we don't know if that would be the case. We write science fiction, but that doesn't mean we can actually predict the future. (Indeed, it's a given that just about any science fiction future will eventually be contradicted by reality, either by new scientific discoveries or just by the calendar catching up. It's not just a problem with media tie-ins.)
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