If they serve the same purpose, then would it be possible to just use one file? I'm thinking of the adage, "A man with one watch always knows the time. A man with two is never sure."
Otherwise, I think we need to know a bit more about the files to know how to handle certain issues. For example, what if they're config files and File A has one setting and B has another? How would you want to synchronize that?
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