Yeah, I noticed.....

Sorry about that, it should be possible for you to examine a file from your original player, and the same file from the cloned player with a hex editor, and try to work out what changes have taken place, write some sort of quick program to fix it, then run that on the cloned Empeg. If you know exactly what you are doing, already have a build env set up then this would be quicker.

Not all files that were transferred are messed-up. Could it still be possible that some files would have gotten corrupted if they were interpreted as text and others were sent ok without being modified to text? Or, would all the transferred files have been corrupted equally?

I think all files are probaly messed up in some way, the differance may be that the ones that won't play have corrupted data in the frame header, while the others just have extra or missing samples depending on where the data occurs.

I'm new to FTP, so could someone tell me how to force a binary transfer and I'll give that a try? Is that just something in the settings?

If you are using a text mode FTP program then typing 'bin' normally works. If it is a GUI tool then there is probably a button with ones and zeros on, or something like that, or an option hiden somewhere in the preferances.