This has bitten me many times, specially if you are running services as different user or require to extend the file limits.
Everytime there is update it replaces the file and it create the issue of broken services.
Here is simple example of overriding the configuration.
cat >/etc/systemd/system/httpd.service.d/limits.conf <<EOF [Service] LimitNOFILE=500000 EOF -OR- systemctl edit httpd
systemd-delta --type=extended systemd-delta --type=overridden