It wasn't long after that when my Dad went to sea and never came back. 这是强调句型，强调时间状语not long after not。不强调的句子为：Not long after that(=Soon after that), my Dad went to sea and never came back. 通常强调句型的从句由that 引导，但因为被强调的时间状语以介词that结尾，为了避免二个that 连续出现，所以用when替换了that。