What controller platform, ZoneDirector or SmartZone, and version please?
Root (wired) APs don't typically reboot. Could the network they're on be flooded by broadcasts, multicasts, or IPv6?
Does your company do any heavy network load events at around 2:00am? (such that APs can't comm with controllers)
Wait, you used the term "Master", ie Unleashed? Version 220.127.116.11.186 is about ready for GA, so please wait a week,
upgrade, and evaluate again. (but consider the questions above)
AND, be aware that Mesh APs *cannot* act in Master or Standby Master roles in the Unleashed network.
If you are losing Root APs and all Mesh APs on them, you should try to install another wired Root AP that can backup
the Root APs in service now. (and hopefully determine why you have reboots today)