Depends on syntax, see description
M164 S<virtNum> P<0 = dont store eeprom,1 = store to eeprom> - Store weights as virtual extruder SSo as long as you have no P or P0 it is only temporary. In that case changing a value in eeprom will override it as eeprom writes cause a reread from eeprom. Normally does not happen during prints so should be no problem.