On Windows 2000 (on the server itself), go to the Administrative Tools and find Services. Open that up, find ColdFusion Application Server, and tell it to stop. When it finishes stopping, do whatever you needed to do to those files, then start the service.
Or, from a command prompt on the server itself, type this:
net stop "Cold Fusion Application Server"
To start it, type this:
net start "Cold Fusion Application Server"
Of course, you need to be logged onto the machine as an administrator-level user to do all this, but I'm assuming you knew that.
Also, check the hotfixes article:
(Right now, accessing that URL seems to do nothing, but believe me, it was the Macromedia article with links to all the hotfixes for CF last I checked.)
There are at least one or two that talk about the problem you're having.
Hope this helps.