Help please Before I get fired :-(

[JAZZCNC]

I think what is happening is the safe retract Z height set in Fusion360 has replaced whatever was previously saved for the Z limit position.

Well, wouldn't worry because it's nothing you have done unless been messing around with settings within Mach. G-code cannot overwrite the Safe Z height which is a setting within mach3.

But what it can do is set Coordinate offset by using G92 and this will most likely send your Probe routine in to melt down. To cancel this issue G92.1 in MDI.
Another potential problem G-code for probe routine is G43 which sets a Tool Offset. Issue G49 to set tool offset to Zero.

Thou to be honest decent Cam program would cancel G92 with G92.1 when finished.
Likewise, good G-code would Zero tool offsets at the top G-code file before running so if this case then your engineer is at fault, not you.

But all this said I think you'll find in the morning all is well because pretty sure the parameters which get changed by G92 are reset on startup. As are any tool offsets which have not been saved in tool table.

[magicniner]

Your "Engineer" isn't setting his Co-ordinate zero in his code.

Clumsy Bastard!

[Ger21]

Those sound like messages from my 2010 Screenset macros?
Do you have home switches on the machine? Just home the Z axis first.
Otherwise, Jog the Z to the top of the travel, and Ref Z while it's there.
If neither fixes the issue, then your Clearance Plane is too high, like the message says.

[hanermo2]

As ger and jazz said ...

You need to follow the exact same procedure as the previous practice.
In start-up, zero, etc.

For many reasons, a screen that looks the same is not the same.
And yes, this is wrong.