Hi Ben,
complete representation of your map (the one in CCP4 formatted file) is a reciprocal space box of reflections with miller indices being |h|
Converting map (from CCP4 file) into a set of structure factors in a sphere of given resolution is an operation associated with loss of information. Further truncation of resolution obviously results in further loss of information. All in all this means the artifacts you observe after these manipulations are expected.
My understanding is that the loss of information would happen at high resolution (which I want to be filtering out anyway),
Discrete 3D function (map calculated on N1,N2,N3 regular grid) in
reciprocal space corresponds to Fourier map coefficients with indices
|h|