It is correct. It is certain that the person will know they are gone. This is the first conditional.

The lyric "if you miss the train I am on, you will know that I am gone" is grammatically correct as it stands. In this context, the use of "will" is appropriate because it is describing a future event that is conditional on another event happening.This implies that if the condition (missing the train) happens, the result (knowing that I am gone) will definitely follow. Using "would" instead of "will" would change the meaning and create a different type of conditional sentence. This structure implies that the speaker considers the event of missing the train to be hypothetical or unlikely, which does not fit the original intention of the lyric.

conditional sentence