Big Sur Update wiped my /etc/apache2/extra

Apparently modified .conf files are reset to their original state not just during the initial upgrade to Big Sur but also during minor updates.

Your modified .conf files are placed in "Previously Relocated Items n" subdirectories in /User/Shared.

This is the last line of the httpd.conf file:

Include /private/etc/apache2/other/*.conf

To keep your modified .conf files from being overwritten after each update you could put them in the "other" directory. If you have more than one .conf file and there are order dependencies then put those .conf files in a subdirectory of "other" and include them from a .conf file in "other".

Just restore them from the backup you made before starting the upgrade. That's way quicker then searching for them on the upgraded system.

On APFS based systems, remember, your custom files and data are on the “data” filesystem and not on the system itself.

Also, look for a relocated items folder on your desktop in case Apple intentionally set aside your modifications.