Perhaps this will help since I update 7000 customers every month. I DO NOT use Installshield to update already installed applications, I use Winzip to do this.

I create a Self Installing EXE from a ZIP file that updates my customers. This update file is downloaded from my web site and automatically unzips to the folders necessary without any effort or help from us. This way it overwrites the existing files with new ones EXCEPT Data Files!

For DATA Files I never provide them, I always update these files via ALTER TABLE commands.

Buy the WINZIP zip and self extracting EXE bundle for about $50 and put all the files you want updated. It pretty much handles everything for you.

If this is not helpful then perhaps someone has something better.