MC206X can use the Flash Memory on power up. It depends on the setting of the POWER_UP paraemter. If POWER_UP = 1 then it will copy the programs from Flash to RAM on each power up. If set to 0, then it uses the RAM on power up and does not copy from Flash. If using RAM for power-up then it is subject to battery charge issues and program corruption can occur.
There is a button in Motion Perfect to "Fix" the programs into Flash and set the POWER_UP parameter. Always be sure to set "Fixed" before you disconnect Motion Perfect.
If trying to recover a controller that has lost battery charge and the programs have been lost, it is possible to restore the last set of programs that were in EPROM. In the direct Terminal mode in Motion Perfect 2, type POWER_UP=1 and then type EX to reset the controller. During the re-start it will load the programs from EPROM into RAM and run them if set to do so.
Of course, if the programs saved in EPROM are not correct then you will simply restore whatever was in EPROM. But at least it might be a good start to restoring the machine.