The game does not keep track of ships, sadly.
If the campaign has Yamato doing what she did til the day she really sinks (RSRD does), and Musashi doing the same, then you will keep seeing them.
It's a function of the way the game works. When ships disappear over the visual horizon, they become abstracted again as the list for that group in the campaign files. next time you are in visual range, it regenerates the group from the campaign files—regardless of what losses it had inflicted on it perviously.
Hopefully new game versions fix this major problem.
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