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If I am setting up my fuel map to then tune the Ignition map will the ignition advance change the tuned AFR's such that I will need to go back and re-tune the fuel map?
Consider that the ignition timing initially set based on some basemap ignition tables that are "safe" and in the reasonable area. But for discussion purposes maybe consider as a second point an ignition timing that is quite retarded but doesn't cause the engine to misfire.
The ign event takes place after the intake valve closes, so your afr is already what it's going to be regardless of your ignition timing. So no, ignition timing does not affect afr.