If I use the 'Publish to another website (via FTP)' option, how does Xara control and update files against what's already on the server?

For example, I'm looking to add a comments section to one page. One of the comments free software options requires me to u/l a small .php file to the root. If I FTP it up manually, would Xara then see it as an error/unecessary file perhaps?

When Xara uploads (and updates for that matter), does it check all the files on the server and then compare them to the Xara website files on my PC, for example, and then do some housekeeping to delete what it might see any unecessary files? Could I lose the .php file?