It actually ends your patrol, and starts a new one from the supply ship. If you have SHC, it should do this overnight, or two days at worst (unless you are damaged, that adds time).
So it will calculate your renown and tonnage for the previous patrol, and then start you on a new one. The game treats them as two seperate patrols, there is no way ingame to do it otherwise.
I'd think, with some very careful editing of the career files, you could merge the results of the two patrols, so the log books would show only one.
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Luck is a residue of Design.
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