How are you setting it in the gcode file? If you are using Cura in UltiGcode/UM2 mode then you can't set the diameter in Cura - there is no UI for it. And the e coordinates are in cubic mm, so the gcode is agnostic on filament size. When you print, the UM2 uses it's internal filament size settings to figure how much plastic to feed in to get the required volumes.
If you are in reprap mode, then Cura uses it's internal version of the filament size to calculate the e-coordinates in linear mm of filament. In that case none of the UM2 UltiGcode stuff gets triggered, and the printer trusts the gcode as written, assuming linear mm coordinates, not cubic ones.
So neither takes priority. Only one or the other applies, and it depends on the type of gcode you are generating in Cura.
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IRobertI 521
If using UltiGcode the settings in the machine has priority.
If using "normal" Gcode (like RepRap-flavour Gcode in cura or gcode from other slicers like KISSlicer) the code has priority and you will get a message on the display saying that the code will override the settings on the machine.
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