See the thread that Malcolm linked. There's not a lot of question about the original meaning.

The partial song sung by Nic Jones is a corruption and abbreviation of a rather longer song preserved in broadside form. Mrs Notley, the singer from which it was collected, only remembered some of the verses, and not in the original order (though we can only guess in what form the song had come to her). From sketchy comments Hammond made quoting Mrs Notley, it seems she knew more of the song and story than she was able to provide; one line she gave is a direct quotation from the broadside text. In her version, the father encounters the young lover in Flanders, while in the broadside they meet only after the young man has returned to England, so it seems the song had evolved and probably shortened somewhat in the intervening century. (Incidentally, the father was responsible for having him pressed into service, and in the meantime locked his daughter up in her room "in a tower so high.") Although Mrs Notley sang "Flandyke", Hammond corrected this to "Flanders" (as in the broadside) in his notes. Nic Jones also later rerecorded the song with "Flanders".

FWIW, I sing a partially reconstructed version of the song.