I just realized that something about this solution doesn't work as I expected. Checking the patrol fleet some years later I noticed that one of the two patrol orders got canceled.There's a way to do it, sort of.
If you want the fleet to patrol from system A to system C, passing through system B:
The fleet will then queue two patrol orders: first it will patrol the route from B to A, then it will patrol the route from B to C.
- send the fleet to system B
- once it's there, select the patrol order
- while pressing the Shift key, select system A and system C
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