I have this recurrent issue, so I wanna definitly learn:
When I configure, manually, configuration.h, then I compile and uploaded to the board. everything is ok but a lot of time I found new values are not taken and old values still are there, working.
I upload the new configuration useing the arduino ID. After upload finishes: Do i have to issue a M502 command, THEN M500 command? What I want to do is to completly delete old values and upload new ones just to be sure the configuration that is working is what I changed and not some old value messing around.