Mod_Security should not overwrite anything, it only does that when you change a setting like ModSec Rules Profile or Rules ENgine.
It is not mod_security
I mentioned before, it is the CWP Security Daemon that is checking the integrity of the files and overwrites known system files that have unknown edits.
My host (InMotion Hosting) confirmed that to me. Maybe it's their custom security module. I don't know.
The only thing I know is that on a regular basis, my
mod_security.conf file would get overwritten with the default "Include:" path creating a chaos on my websites.
I hope this helps.