In my research on the Phagan family I have found that the spelling of the name "Phagan" was changed to "Fagan" by James Phagan/Fagan, born abt 1797. He was the son of Moses Phagan (1765-1830) and grandson of Phillip Phagan, Sr. Moses also had another son, Phillip Phagan, who did not change the spelling. As far as I have found in my research, James Phagan/Fagan's line were the only ones who descended from Phillip Phagan, Sr that changed the spelling to "Fagan." I have also noticed it spelled "Fagans." I noticed in the 1830 census that James' last name was spelled with a PH but from the 1940 census and on it was spelled with an F. My guess about the reason for the change is that the census workers usually spelled phonetically so it was just spelled with an F, like it sounds, and James decided to continue using that spelling because it was probably easier. I've also heard the reason was the mail, but who really knows for sure?
On another note, there were also some that changed the spelling to "Phagans" with an "s" at the end. Andrew Jackson Phagan/Phagans and his children all spelled their name Phagans.