[EDIT]
It's redundant, I find the same problem here but without final solution:
http://www.subsim.com/radioroom/showthread.php?t=198603
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I have found a single *.cfg file with config entries for destroyed marks. I will compare the versions 7.4.2 and 7.5.0 and adjust the file in 7.5.0 if they are different. I will report here if it works. However if the mod author TheDarkWraith found it appropriate to change it, then there must be a reason
By judging from the look, TWoS is using a map background different from the stock game and also uses different mark styles (e.g. the torpedo line is not a yellow line but a grey - - - - line, I guess all other marks have been redone). I have never noticed missing destroyed marks in TWoS (I see them during campaign), but they are not saved together with supermarks IIRC; I will take notice next time I sink a ship...
Overall the problem is a very small one because the Captain Log will report all sunken ships anyway, and if need be one can still put a manual mark - or supermark - for sunken ships.