What's removing stuff from /var/run at reboots from a fedora machine?
The software should define what directories it needs in /run (which replaced /var/run in Fedora 15) by placing a configuration file in /usr/lib/tmpfiles.d. During the boot process, systemd-tmpfiles populates /run based on that confguration.
/var/run is usually mounted as
tmpfs, which is a partition mapped into your RAM. Obviously RAM gets cleared on reboot, so do all tmpfs file systems.
You should consider storing your application data on a persistent file system e.g. mounted on a hard disk.