Quite strange, but when I went into the patrol and career cfg files as Danlisa suggested, somehow [Patrol 003] was squeezed between two separate lots of [Patrol 002].

I deleted [Patrol 003] and the second [Patrol 002]. In addition, I noticed in both the patrol and career cfg that there was no "Dead" or "Alive" line, but there was a "Finished" line that had "true", whereas all the other similar lines were "false".

I took the opportunity to change that line to "false".
Lo and behold, my 2nd patrol showed as a saved patrol at Wilhelmshaven, not "Dead". I am currently in progress in my 3rd mission, having already sunk 24,000 GRT of enemy shipping.
Special thanks to Danlisa

, but thanks also to the other contributors.
Cheers,
Tim.