First, I don't see why the text/binary file distinction should have anything to do with assigning file names. All you should need to worry about is preserving the original file extension, since this always matters for windows apps, and if you happen to shorten any names, make sure you keep track of the original and what it was shortened to, in case users think their original names had some importance.

Maybe what you want is a two-stage backup process, which would be easy to script sensibly in perl:

1. for a specified list of directories, create a corresponding set of zip files using a recent version of a good zip utility; make sure that easy names are assigned to the zip files, and make sure that internal subdirectory structure and file names are preserved.
2. use your existing backup utility to backup the zip files.

You would probably want a nice tabulation or database as a side-product, so when some poor shmuck loses his file, you can figure out which zip file contains it.

Have a look at perlfunc:rename. It seems to work for any long filename I tried (Upto 250+chars) under NT4 and NTFS from AS 5.6.1.

to add to the existing answers... consult the docs

>perldoc -q rename a file
Found in perlfaq5.pod
  How can I reliably rename a file?

            Well, usually you just use Perl's rename() function. That may
            not work everywhere, though, particularly when renaming files
            across file systems. Some sub-Unix systems have broken ports
            that corrupt the semantics of rename()--for example, WinNT does
            this right, but Win95 and Win98 are broken. (The last two parts
            are not surprising, but the first is. :-)

            If your operating system supports a proper mv(1) program or its
            moral equivalent, this works:

                rename($old, $new) or system("mv", $old, $new);

            It may be more compelling to use the File::Copy module instead.
            You just copy to the new file to the new name (checking return
            values), then delete the old one. This isn't really the same
            semantically as a real rename(), though, which preserves
            metainformation like permissions, timestamps, inode info, etc.

            Newer versions of File::Copy exports a move() function.

~Particle *accelerates*

The command in the backticks isn't portable, of course, but since you're running into a Windows-specific problem that's unlikely to be a concern here.

        $perlmonks{seattlejohn} = 'John Clyman';