WHY ALL CAPS? That's impolite.
The two microcontrollers probably have different jobs to do. One looks after the LCD, and the other one does "something else". You haven't provided any details on what this controller does that may help us help you.
Why are you copying from one to another. Are you attempting a "firmware upgrade", or did you have an un-progrmmed board somehow?
So copying to one of them worked (the one connected to the LCD) and the copy to the other one didn't. Which is which? Do you know?
Time to get out the oscilloscope, schematic diagram and do some proper hardware debugging. Or find someone else who can. There's no easy way apart from that.
How big were the S19 files? What were the minimum and maximum addresses encoded in those files? The question is, did you copy all the data from both of them? The MCF51QE128 has 128k of Flash. The MCF52258CAG66 has 512k, so the addresses in the files should cover those ranges. Of course the programs in the Flash may be a lot smaller than the maximum, but the programmer should have copied all of it including the "erased Flash", unless there's an option to prune this.
If you don't know how to read S19 files, then read this:
https://en.wikipedia.org/wiki/SREC_(file_format)
Tom