I've found that in many cases I can use FTP on a FrontPage site without harming the FrontPage extensions.
* In a separate folder with no FrontPage files in it, I can FTP to and from the folder as much as I want and FrontPage doesn't care.
* In a separate folder I can install and run a PHP script such as phpBB or SMF and FrontPage doesn't care.
* In FrontPage folders on the site, I can FTP new versions of files that FrontPage doesn't use (for example webcam pictures, PDFs, and streaming media files) and FrontPage doesn't care.
The main activities that FrontPage DOES care about are
1) Rewriting the htaccess file and
2) Rewriting the files associated with the features using the FrontPage server extensions.
The Microsoft page below contains a chart that shows the features that use the server extensions. Our column is the column labeled "with server extensions for FrontPage 2002."http://www.microsoft.com/office/frontpage/prodinfo/servers.mspx