You must be referring to the check box labeled something like "replace current version" where you browse for the zip file to upload. You want to say "yes" because you're uploading a new version - the one that was replaced will drop down into the archive of your mod.
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"You'd be surprised how many people violate this simple principle every day of their lives and try to fit square pegs into round holes, ignoring the clear reality that Things Are As They Are." -Benjamin Hoff, The Tao of Pooh
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