It probably means nothing at all; Carthy sang ba, not va, as I mentioned earlier (the sound is the result of a vocal mannerism).  I suppose I could quote the following, which I didn't have at the time the question was originally asked.  In a discussion of The Elfin Knight (Child #2), Bronson said, with reference to a blackletter broadside of c.1670, The Wind hath blown my Plaid away, or, A Discourse betwixt a young [wo]man and the Elphin Knight:

"..Without the testimony of the tune, however, we do not know how to read the first refrain-line.  The other (second) refrain-line gives a norm, tetrameter iambic.  But the first, "Ba, ba, ba, lilli ba," has only six, instead of eight syllables, and the accents are uncertain.  The scansion would be settled instantly by the tune, but not the meaning of the line, if it had a meaning.  Supposing it were meant to suggest the horns of elfland (whence the knight fetched his instrument), we should then know how they sounded.  By the merest chance, a traditional version of this ballad was sung in West Newton, Massachusetts, about 1870, to a pentatonic tune with a hornlike second phrase containing the same number of syllables, thus:

Blow blow blow ye winds blow

It may be only a coincidence; but since the version is traditional, it is at least a curious coincidence.  When we find in Scottish tradition, in the first decade of the present century, a form of the ballad to another tune but with twelve stanzas of the earliest text still recognizable, and with refrain-lines almost identical, we begin to suspect a persistent continuity, viz.:

Bo ba ba lee-lie ba

But the sense remains obscure...  mere common sense prompts the conviction that originally neither refrain nor burden had anything to do with this ballad.  No one, making a song on the riddling theme, could have thought up the refrain on rational grounds, or have supposed it appropriate."

-B.H. Bronson (The "Child" Ballads: Fractures in Tradition, paper of 1966)

Bronson goes on to suggest that the lines derive from an earlier, quite different song of the same title, which is not identified.  He also quotes a number of variants of Child #2 found in the United States, which have taken nonsense refrains to a whole new level, Keedle up a keedle up a turp turp tay, Tum a lum a do, castle on my nay being one!

Malcolm