Sometimes it takes time for the message to appear. If you dont get the sunk message, you might have to wait some time, or send another torp to finish the job. Im not sure how TMO works with flooding, but I know in RFB it can take hours to sink, sometimes even more. If TMO is like stock, if its going to sink, it will sink in like, 10 ingame minutes.
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I used to be a huge submarine guy but now I'm a huge submarine girl ¯\_(ツ)_/¯
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