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The orders are for 7th Flotilla (Konigsberg) only. In GWX your first patrol starts August 1, a month before the war begins. The other two flotillas only have you set out and wait. The order to sink ships can be ignored. In fact pretty much any order in SH3 can be ignored. You can do a quick turnaround (just start the patrol and end it again). Then you will be bumped to 28 days later and you can start a real patrol just a few days before the war starts.
Your patrol orders don't really mean much in this game. You can do anything you want. Of course you might have ended up at AN51 and sank some ships, only to find yourself the enemy of everybody because they were still neutral, the war having not started and all.