Just to expand on what andypugh has mentioned, if returning to absolute zero (G53 Z0) Axis also takes into account any G43 offsets present at the time G53 G0 Z0 was executed, so the tool in the backplot will appear to be at TLO units lower than the expected Z position.
When I try to home the Z axis it always changes the DRO and backplot to Z0, regardless of where it was previously, and rewgardless of where the mill is.
Then I suspect you will also need to redfine your Z-axis max and min limits on your INI file to be max = 0 and min = -5. When you home in Axis it is assuming that you want the current position of the cutter to be re-referenced to Z=0 as defined by the range of motion specified in your INI file.
After you get this straightened out you shouldn't need to go back and manually rejig your G-codes. It should all just work