Some ships evaded the British fleet. Napoleon sailed back on the frigates Muiron and Carrère. It took them five weeks by a circuitous route to reach France.

Source: Louis Antoine Fauvelet de Bourrienne (his private secretary) Memoirs of Napoleon Bonaparte Vol I

Thanks to /u/estherke, I can name the ships, the muiron and the carrère, which survived the onslaught of the Battle of the Nile. Remember that just because a battle happened, doesn't mean that everything was killed, captured, or destroyed. The ships would have sailed around to another port or just away from Nelson in order to survive, and from there, there is nothing more to say than luck. By luck and good navigation, the French were able to slip by the British. I wish that there was more to say beyond this, but luck was on Napoleon's side much of the time.