Loads from wrong directory

I recently made extensive changes to a site. In order not to disturb the existing site, I did all my work in a subdirectory. When everything was debugged I (1) copied all modules to the main directory and (2) used phpmyadmin to edit site url and home to point to the main directory.

Everything seemed to work fine. I made a change to headr.php. This change took effect on my landing page but not on the subpages. On the subpages it appeared to fetch header.php from the subdirectory.

I verified this by renaming the subdirectory. This causes an internal configuration error.

I copied the new version of header.php to the subdirectory and now everything works again.

But I don’t understand why the server sometimes fetches from the subdirectory and not the main directory. I suspect there must be something else in the database I must change in addition to site url and home. But I don’t know what.

Any suggestions would be much appreciated.

Thanks,
Bob