...Cleopatra was a consummate stateswoman and, above all, a survivor. She would not abandon Caesar Antonius willy-nilly. She would not risk her head for a few ships. Egypt didn't lack gold, with the lands and monopolies she obtained from Antony she was incredibly wealthy. As Octavian's efforts against Pompeius clearly demonstrated, navies could be destroyed and rebuilt. She would either sit the battle out and make her escape after defeat (as she did OTL, obviously expecting to sex or bribe her way to live another day afterwards) or, at the very most, only ditch Antony after having secured an understanding with the other side. She would have no wish to, however, given the superiority of his position and person vs Pompeius and Agrippa. .
I concur Cleopatra would only have ditched so early in order to flee the Mediterranean World entirely. IIRC she planned to go to India with her children. Please consider the possibility that in your fine ATL that she successfully did this very thing. It would help justify Sextus Pompey retaining control of a larger military than would otherwise be needed.....lest the evil Witch-Queen Cleopatra return to seek revenge on Rome. Hell it could even justify a subsequent Indian Adventure for the First Citizen of Rome.
Hero of Canton