If I remember correctly I did virtually the same for my Wolves at War campaign. In order to align Campaign date with patrol start I increased days spent in base after docking. When I startet the next patrol departure was exactly x days later with x being the value from SH Commander.
Since I'm not using Milkcow Mod I can only guess its the same if they are treated like a base - but this is only guesswork.
So why not give it a try - you can always reload an older save game.
Phyl
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