The song didn't appear in the "early" references to chanties -- again, perhaps it wasn't yet in existence, or else known in the "Across the Western Ocean" form. Later on in the writing, it appears like crazy. It may be because the song got really popular to sing...OR the writers about chanties really loved the idea of it -- including the elegance of ending their collections/articles with it... and liked the mileage it gave as something that could be discussed with blurbs about how it was the "last" chantey sung on a voyage, etc.

Anyways, the next reference I'm turning up is in a source introduced by Lighter, a New Zealander newspaper:

1896[Aug.]        Unknown. "The 'Chanties' of Sailors." _The Matura Ensign_ (13 Aug. 1896).

And when the homeward voyage is over...the crew have to wash her down and pump her out....The particular chorus runs thus:

I've earned all my money, and I worn out my clothes,
Leave her, Johnnie! leave her!
Oh! shake her up and away we goes.
Leave her, Johnnie! leave her!
We'll shake her up from down below,
Leave her, Johnnie! leave her!
We've stuck to her through sun and snow,
Leave her, Johnnie! leave her!

This of all the chanties is sung with the most unanimity and cheeriness...