Can I change the referee once the letter of reference has been submitted?
The importance of letters of reference is covered in many other questions on this forum, and I won't discuss it here.
As for changing letters of reference: Most systems are set up to just take as many letters as are submitted. They will then all become visible to the selection committee. In other words, there is probably little you can do about the already submitted letter short of writing to the selection committee to disregard that one letter -- but that raises so many other questions that I don't see that as a winning strategy either.