Well, I was so unhappy with the problems I was having with .DS_Store files and broken folders that I created a quick and dirty Mac OSX program to fix the problems. I have finally packaged it in a DMG image so other power users to make use of it.
Keep in mind that this program was only designed to work with Linux based NAS systems that support the FTP service like those provided by QNAP. It only runs on newer Intel versions of Mac OSX such as 10.7 or later.
WARNING: carefully read the enclosed PDF documentation before using. The program is believed to work correctly but has not been tested extensively other than on my NAS under conditions specific to my setup. There are some features of the program that may not fully suit your purpose and some that could damage file links. Back up your data before use or copy it to a new share for testing first. Source code is provided should you want to twiddle with some bits.
The Mac Finder and Mac based backup programs may not work correctly due to problems this program fixes. Doing a direct backup using the USB copy functions to an external disk formatted in EXT3 or EXT4 format will fully preserve your files. If you copy the NAS files to either Mac or Windows format drives, not all the file information may be intact.
Click this link to download the DS_Store_Cleaner program, source and documentation.