You need to consider all of the volume that the gas initally is in and will settle out in. Essentially, when the compressor is running the gas is flowing from one system at P1/T1, to another system at P2/T2, etc. You need to add up all the volumes and masses of gas in the system at the various pressures and temperatures to estimate the total system mass. Depending how much the pressure/temperature changes through the system will decide how individual calculations you need to do.
The compressor internal volume normally wouldn't be considered as when the compressor trips, the discharge check valve will close and the gas within the compressor equalizes out through the suction. This might or might not be applicable to you depending on your system.
At settle out, you have still the same mass of gas but it will all be at the same pressure or where the density of the gas (eg. settle out pressure) * system total volume equals the initial mass of gas. If part of the system(s) is filled with liquid and that volume doesn't change, then you don't need to include that.