I just got these messages. From an ArchLinux thread, these aren't files, they are kernel configuration parameters, see sysctl.d(5). "systemd-sysctl.service(8) reads configuration files ... to configure sysctl(8) kernel parameters." These ones are settings under /proc/sys/net/ipv4
The files /etc/sysctl.d/50-libreswan.conf and /usr/lib/sysctl.d/50-default.conf specify these parameters. Maybe systemd-sysctl.service has default settings for these and it warns when configuration files override them when it parses these files during certain updates. Both files are provided by Fedora packages, systemd "System and Service Manager" and libreswan "IKE implementation for IPsec with IKEv1 and IKEv2 support" respectively.
So, I don't think you need to worry.