Once the individual state filing deadlines have passed, it’s likely that Trump/Vance would have to remain on the ballot. But this is one instance where the Electoral College helps, because the election is not for the candidates themselves, it is for electors who support the ticket. And the final certification of electors is up to each State Legislature.
So, if God exercises His Ultimate Veto on Trump’s Presidency, it will be commonly understood that Vance would take over the ticket. He will pick a new VP, and any former Trump/Vance electors would likely cast electoral votes for Vance/Chesterfield instead. While it is possible that State Democrats might challenge this, it’s also absurd to force electors to vote for someone who can no longer take office, so it’s likely that States would give their blessing to the substitution. Particularly if Harris is the overall winner regardless, and the Republican EC votes are simply for the historical record, and have no effect on the outcome.