This is not an issue.
First of all, Rubio is eligible to be VP even if he and Trump both remain residents of Florida. The relevant portion of the Constitution in Article II says:
The Electors shall meet in their respective States, and vote by Ballot for two Persons, of whom one at least shall not be an Inhabitant of the same State with themselves.
(This was superseded by the 12th Amendment, but it keeps the same requirement.)
This only means that if Trump/Rubio win Florida, which would be likely, the Florida electors could not vote for both of them. Florida has 30 electoral votes. So if:
Trump wins with at least 300 EV: the 30 Florida electors just vote a blank ballot for VP, and Rubio still has enough EV to be elected.
Trump wins with 285-299 EV: 15 Florida electors cast a vote for Trump and a blank for VP, and the other 15 cast a blank for President and Rubio for VP. Both still get at least 270 EV and are elected.
Trump wins with 270-284: the Florida electors cast a blank ballot for VP. Trump is elected by the EC and the VP is chosen by the Senate, which almost certainly has a Republican majority in this scenario. At worst the Senate will be 50-50 and the VP will remain vacant (Harris can't break the tie -- this isn't legislation) until Trump's inauguration, after which he nominates Rubio for VP, and even if the Democrats have flipped the House, it's difficult to envision them not confirming Rubio.
Trump loses (Biden has at least 270 EV): it doesn't matter what Florida's electors do.
