I always use THIS free online site for checking files, even though I have Kaspersky, there are times when a second opinion is warranted :)
I really wouldn't recommend playing around with the system files, and besides, most DLLs would need to be unregistered, removed then re-registered (usually). You could introduce massive system instability.
How about creating a System Restore point, update DirectX and check. I can't believe that updating would affect his program - that's the whole point of keeping your system up to date, surely.