that you have followed the accepted (and sensible) practice of publishing your web to your hard drive first - then opening it from that copy and publishing to the server?
That way, whenever you want to make changes you should open the hard drive (local) copy, make the changes and save them, and only then publish the changes to the server. It's not generally wise to work 'live' on the server copy.
By adopting that working practice you'll ensure that both your backup and server copies are always in sync, and FP will faithfully update the server directories as and when it notices changes.
The new version of FP (FP 2003) has some enhanced tools for managing server and local copies, and it's a one-click operation to synchronise both versions.
In your case it might be an idea to get your local copy completely up to date, and then delete the server copy entirely. When you've done that, publish the web to the server afresh, and you should have no further problems.