Hello,
I wrote a simple command line program in Java to change the prefix of C++ classes, which you can find on my github:
This tool will both rename files and refactor source code with new class references. The description in the readme is quite detailed so please take a look there in case you’re curious 
I didn’t find anything to rename multiple C++ files and after working on it I figured out why. I have the feeling I reinvented the wheel but it has been nice to write this tool as I faced the troubles you’ll get into when you need to rename classes in Unreal.
Bugs are welcome when you do such dangerous things, I just wanted to push this code on github as it might be useful, I tested it in the editor and in a packaged game and things worked.
Just bear in mind, I’m sure there are so many edge cases I haven’t taken into account for the limited time I can dedicate to this, but I hope it will be helpful!
Cheers