You need to start with a basic understanding of what is
being presented to you and how to get to the underlying files
with no confusion about what is there.
Linux is case sensitive. You can have multiple directories
that all map to the same name under windows.
Samba (the software that lets Linux present drives to Windows
systems) needs to alter Linux file and directory names so they
appear as legal dos/windows file names. Something this alteration
can cause great confusion when you accidently duplicate the names.
So, you NEED to start on the Linux side to get to the underlying
file names to resolve it.
Do you have a command line login to the box?
Do you know how to mentally map the Windows share
to the underlying true Linux path?
Are the familier with the "ls" command for listing files?
Are you familler with the "less" command for looking into
the contents of files?
Anser the above, and give me directory and file names that
you are trying to resolve and we'll take it from there.