PP&M "peterpaulandmarificated" almost every song they recorded, especially in the early years. All were changed, some beyond recognition. And yes, they registered their versions, as did many other performers. It's a real chore to sort out and prove which claims are valid and which are not. In working on the Rise Again songbook we found we had to pay royalties on a number of songs I could prove were traditional, but it was just too much of a hassle to try to fight it - especially with Carter Family songs, and songs collected by the Lomaxes.
-Joe-