Just in case this has been problem for anyone else I have found a workaround.
If I start Mach
Reference
go to zeros
load Gcode
jog my axis and zero the axis to make the new offset
regenerate the toolpath to see the updated offset.
Now previously if I shut down at any point after this I would not get asked if I wanted to save new fixture but I have found that, if after regenerating the toolpath, I press the zero buttons for each axis (even though they are already at zero) when I shutdown I am asked if I want to save the new fixture
If at anytime I regenerate the toolpath or change display mode I MUST press the zero axis buttons if I am wanting Mach to ask if I want to save.
Hood