PHD turns all bad pills in good pills.
I had two "I Can See Forever" pills in a run with PHD.
What is the negative pill that turns into "I Can See Forever"?
No pill is converted to I Can See Forever by the PhD or similar effects.
It is, however, possible for the same pill to appear twice in the same game. In this case, your game would have had two different pills with I Can See Forever.
Source: http://bindingofisaacrebirth.gamepedia.com/PHD http://bindingofisaacrebirth.gamepedia.com/Pills
PHD turns all bad pills in good pills, but there are neutral pills too, so effects like Puberty, I can see forever, Bad gas, 48 Hour Energy, Bombs are key and Pheromones won't be converted.
You can still find them after collecting PhD.