I've run into this numerous times.
The webserver is likely caching the files. A reboot of the server would reveal this. Of course you could simply restart IIS if it is a Windows Box.

I've also seen issues where I make a change to a file on the website and some time later the file reverts back to a previous state. It is like the file has not been written to disk and is still in the page file. You check the file and it shows the changes. Restart the server and the file goes back to what it was before. Very frustrating when the server starts throwing up 500 Internal Server errors because only some of the files have saved correctly.