Support can generally help rebuild the INI files. The backup would have to predate the issue of course if you're going to go that route.
You might also be able to remove PXE from the server (s) clear out the PXE files, then re-add it, which would force the recreation of those INI files, unless they're corrupt at the source. You might also try adding another PXE server just to see what it does.
OH. OR you could build a lab with the same installation, and then CHECK the INI files in that lab against what you have. There should be a KB about the INI files that DS 6.9 uses to list the PXE preboot options.
I'm assuming you can rebuild your PXE preboot options, yes? If you've never built one, even if they're in BootWiz as an option, then they wont show up on the list. Try building a new one, one for Linux, one for PE x86, one for PE x64 - see if any/all of them show up on the PXE boot list and be sure to name them uniquely so you'll know when they show up.