Another "canned program" horror story!
BEFORE you restart Apache, recreate your VirtualHost section(s) and put them in a vhost.conf file and modify EVERY httpd.conf (unless you can determine which one will be the one used to restart) to include the vhost.conf file, e.g.,
At least that should maintain your VirtualHosts while you sort WHICH httpd.conf that is being used.
Include conf/vhosts.conf #assumes that it's colocated with the httpd.conf in Apache's conf subdirectory OR
# Include /home/path/to/vhosts.conf
Which one? Pop the foo directive (an uncommented line containing only foo) in each httpd.conf, one at a time, and try to restart Apache (Apache will not understand foo so it will not start). When it does not start, THAT is the httpd.conf Apache is looking to for its startup so quickly remove the foo directive and restart.
Backups? 'Nuf said.