I have been to each DC and can confirm that this location doesn't exist, I have no idea how this is all pieced together. Are there any ways in which *.kix script files are hidden within a *.kx compiled file?/ Thats my only other explanation
No, not in the way that you mean.
*.kix files are plain text, so of course any KiXtart script can create another KiXtart script file on the fly and CALL it. However your users won't have write access to the netlogon share so it won't be true in this case.
Another technique is to include multiple "scripts" in a single file as discrete code and then get the script to create new instances of itself by using SHELL or RUN, passing parameters to control what code is executed in the new instance (kind of like forking in other languages but without preserving the run time environment).
I don't think either of these applies in your case, it's more likely that someone has moved, renamed or deleted the script directory and that change has replicated to all your DCs.
