Well, you might consider a different tool for doing backups... But maybe there is a simpler method where perl can help. I'm not a windows officianado, but here are some ideas.

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.