publish1 being in a URL does not mean there is a directory by that name. As you suggest the publish1 directory no longer exists, eZp might be finding that word in site.ini, a reused database table, or a rewritten URL.
Check subdirectories within "settings" for files which mention "publish1" (find settings -type f -print | xargs grep -i publish1). Check your web server URL rewrite rules (/etc/httpd/.../httpd.conf ?). I don't know what DB tables might have such a URL path; I mentioned it because your phrasing did not indicate that the DB was cleared out.