Clearing the faults does not "Clear the RAM".
You can connect to the processor and stop the CPU then in Proficy ME use the Target > Online Commands menu to clear all memory.
But as you say this system uses an EEPROM and if the OEM has set the system to "Copy Logic & Config" from there on power up, cycling power on the CPU rack will do the same thing.
But then it just may be that it looks to them that some retentive memory may have some incorrect data in it that needs to be cleared.