If you are using FrontPage to build your website and you upload or delete content using FTP, you are bypassing the management that FrontPage performs for your website. This can potentially break your Website.
FrontPage manages the special permissions on your directory. These permissions must be added to the directories in your account. Write permissions, if necessary, are also handled by FrontPage. If you upload using FTP, these permissions may not be applied correctly.
There are also several hidden, internal directories in a FrontPage Website, which contain meta data that describe how the Website is constructed. Some pages within the Website rely on this meta data to render the pages correctly. When you upload the data via FTP using FrontPage, this meta data doesn't get updated and your Website will no longer work properly.