AFM Data should indicate the source, be it flight test, extrapolation of flight test, first principles, etc.
First principle performance data will be based on physical laws and a number of assumptions. The accuracy will be in question, but some spot checks of the data may have been completed in flight test to confirm reasonable accuracy.
Flight test data in the AFM may have a line drawn through or beyond data points that is based on the first principles, so in some cases the "academic" difference between the two is minimal.
Matthew.