Not sure I understand your question.. (your wording is a little unclear) so let me say this.. Whenever installing mods you should ALWAYS merge any files the mod has in common with those already in your store.. ALL of the files in common.. Not just the ones you THINK might be different. (If they are included in the fileset, then chances are they ARE different than your store files..) You should be comparing ALL files and merging and differences found..
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