Actually, it's not SH3Cmdr that is getting confused, it's simply the player.
Robin40, by returning to base you have effectively, as far as SH3 is concerned, ended your patrol, regardless of whether or not you penultimately saved it "in the water". As SH3Cmdr merely reads the SH3 game files, this is why it reports your career as "In home base before patrol X".
You need to "Save and Exit", as CherryHarbey recommended, to save mid patrol. Then SH3Cmdr will report your status as "At sea during patrol X" and crew transfers and Kaleun retirements will not occur.
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