Can a professor alter the syllabus when calculating a final course grade?
I would argue that an instructor has the right to deviate from the syllabus's method if it does not unfairly penalize any student. 

I had this happen recently when I told a class that the weighting of the final exam was different from how it was calculated on the syllabus. Because the change benefited everyone in the class, except for one student who was right in the middle of a grade range (and was only disadvantaged by about 1 point out of 1000), and therefore was not hurt by the change, I kept the more beneficial weighting.