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Since you know how to hack the registry, I'd try locking permissions on the .flt association once you have it set the way you want. Not sure it'd work, but it's worth a try.
I tried denying the SYSTEM from being able to SET the key but that didn't seem to make much difference. I wonder if I just need to DENY the SYSTEM from being able to do anything to that key ?
Ok here's the solution to this.
It turns out that Illustrator deletes and resets the .flt file extension key and the Adobe.Illustrator.Filter key every time it is run. Removing registry permissions for system didn't work, neither did removing them for owner/creator.
It seems that the change happens as "me" - the person logged on. As I'm an administrator anyway, I was able to remove all rights for every user (including me) except administrators, and then change the administrator rights to allow everything except set and delete.
So the .flt file extension key is essentially locked down completely now, and the problem is solved. However as the owner of the key I can still get in and change the set/delete flags if I ever need to change it again.
Thanks to Harron for giving me the hint on the right way to pursue this.
Thanks for getting back to us with that info, Chrisell99.