As a colleague of mine once said at a conference about an entirely different subject: "If you are not yet confused, you are not yet informed".

We seem to have a tangled history of songs on at least two themes:
1. the ballad, with its story of (probably) rape followed by later marriage, most versions of which don't mention Cowdenknowes at all, being better identified as The Ewebuchts; and
2. the lyrical lament by a girl (or recently in the Revival a man) about separation from Cowdenknowes where she or he herded or milked the yowes.

Both themes can be combined in the same song, with the girl in the ballad being married but still wishing to be back with the yowes, but I'm not at all convinced that they belong together.

The Watersons' version of the lyrical song is clearly either an extremely abbreviated extract, with trivial changes, from The Lovely Northerne Lasse as printed in Child's 217 Appendix, or else a separate descendant from a common parent; anyway with only the word "deceived" to give any hint of an explanation for the separation.