Just seen this thread. I think the best thing to do to settle which is the definitive version is to ask the good denizens of Holmfirth what they actually sing. (Pity, I used to have a mate from there years ago but we've lost touch, or I could have asked him.)
With that in mind, the only recording I've heard is by the Holmfirth Rotary Club, and they definitely sing "shepherd dear". I think they do sing "lands" rather than "lambs" but of course these two words sound very similar when sung, so it's difficult to be 100% certain. And yes, they do sing "pratty" rather than "pretty", and the song is entitled "Pratty Flowers". So that seems to back up the Captain's theory that these are the correct words.
But as to whether the Watersons were 'wrong' to use slightly different words is difficult to prove, because the song's origins are not entirely clear (the Ammon Wrigley stuff I posted as only one explanation; there are others). Holmfirth may have laid claim to it as their anthem, but for all we know it could have originated elsewhere in Yorks (or even outside the county... maybe even Lancs - shock horror! ;-)), and there could be slight local variations as there are with many old songs. Maybe the Watersons got theirs from East Yorks - I don't know if it says on the album sleeve where they claim to have got it from (does it? anyone know?)