URET Android Reverser Toolkit v1.1

[Mkz]

I think the answer to your question depends on this: what is the source of the files?

Since Windows does not allow dealing with duplicate case-sensitive files, you can't have the source files directly on the filesystem. There are some registry settings and hacks to partially enable that support, but for the NTFS part only and not for Explorer or other windows portions. You'll need to use Cygwin or other Linux compatibility layers (see some info here: hxxps://superuser.com/a/430645 and other answers on the same question).

Now, assuming you'll need to forget about having the expanded files on the disk, what is your scenario?
Do you have a jar with A.class, a.class and need to produce a zip with A.java, a.java? Or a .dex and the need to produce a zip with A.class, a.class? etc.

Note that I'm not saying I'll be able to provide an answer, I'm just stating that you should clarify your actual need