Z Offset (probe & endstop) - Relationship between stock/mod config

[Juszzy]

Hey All!
I apologise if this has been covered in other topics/threads.
I have a general understanding of the relationship between endstop and probe. But i'm very new to Flashforge and it's probing.
Calibration of probe vs endstop and when to use each.
In my other printers i would calibrate the Z probe and never had to calibrate the endstop (being physcial endstop bed slingers) and if i did move it, i would simply adjust the z min or so.
I made the mistake of doing a probe calibration and after doing so, it threw an out of range error. Completely screwing everything.
I guess, i'm asking if there is a general rule of thumb in how best to approach this when Z probe and endstop calibration are an option. Would i just not use probe calibration and focus on the endstop and then make microstep adjustment via slicer or tuning menu? And then maybe apply the Z probe if i was to use tuning menu after the endstop calibration?
And does any calibrations performed in stock firmware carry over to the mod? (I went back to stock to autocalibrate to get the print job out)
Thanks in advance and apologies again if i have echoed previous questions.
Cheers!