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I just figured out why this rule exists!
It's to prevent you retreating a leader with a single ship, then moving all the remaining fleet with the next system activation, hence enabling ships to move multiple times per turn.
You can still get an effective second move through a retreat, but only to a friendly or neutral system.
It is to prevent a second retreat in the same turn.
If you had 2 leaders in the system, retreated one or more ships, but not all you could technically do this again.
Except that the rules specifically say that you cant retreat twice.