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bcabalic - If I understand your inquiry correctly, you want to use FTP to copy your webfiles to the machine that is running Mozy and have Mozy backup those files. If that is the case, then the answer to your question is Yes. A couple of items that you need to be concerned with is the FTP session needs to complete before Mozy starts the backup. Also, the validation of the data being copied by FTP to the local machine (the machine that is running Mozy) needs to be done by you.
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