It is a matter of absolute certainty that the pigmented lesion above the eye was surgically removed between early 1940 and late 1941. The point, of course, was to do it slowly without (pardon the pun) raising any eyebrows that something was awry. It was a phenomenally successful effort, and likely reinforced Roosevelt's belief that, when it came to hiding his health problems, he could get away with almost anything (and he did!).
Before Ross Mcintire began carving at the lesion, there had been some trauma to the area, with a scar within and lateral to the eyebrow seen in photos as early as 1915. This scar shows up in some some photos in the 1920's, is especially well seen in photos of FDR at his first inauguration, and shows up throughout the 1930's.
This was initially a source of confusion but it answers are a bit clearer.
Geoffrey Ward's first book on FDR "Before the Trumpet" (p. 145) describes an incident where the nine-year old Franklin sustained a deep cut on his forehead from a falling curtain rod while on a ship with his father. The point was that stoic and proud FDR insisted that his father not be told, rather asking for a cap to cover the wound. This incident may be the source of that scar. It is also clear from a few photos that another well known skin lesion, the benign waxy mole on his right cheek was, at one time, a considerable cosmetic eyesore. This may also have functioned in sensitizing him to the appearance of his face. It is also apparant that, sometime in the late teens or early 1920's some minor cosmetic reduction was performed. The photographs below are ample testimony.
The old scar continues to be evident in some photos after 1942. It could also be speculated that McIntire the old scar as a portal to treat FDR's mew and malignant problem.