Based on standard JDE naming conventions these are not files but programs. A "P" prefix indicates an RPG program and a "J" prefix indicates a CL program.
Are you referring to moving the source code for these programs or moving the object code that exists after they have been compiled?
If your moving source code, you should use the SVR to copy code from one environment to another. I don't believe JDE World has a method of moving object code.
If you have multiple environments on the same AS400 you should not have to copy any programs. Just make sure the program library containing them is in both environments (which is normal).
Sounds like you might need to contact someone in your IT dept or to read the JDE World Technical Foundation manual. That should make a lot of things clearer.
Tony's right the programs shouldn't need to be copied if the library structure is setup correctly. However some environments have different programming needs depending on the reason for the environment.
But also based on the names of the programs the P55 and J55 are probably custom programs since again the naming conventions dictate that the 55 system number is reserved for user written programs. With a name like P554748 it would lead me to believe that someone came in an cloned an existing P4748 and customized the code for this shop or this specific environment.
It sounds like someone copied a logical file so that it was still pointing to the original physical file. It's always best to recompile logicals to ensure they point to the correct physical file.
I replied on the X0028 thread earlier.
It sounds like you might have people with a limited JDE technical background administering the system there. These problems ought not to occur under normal circumstances.