Failures on updates can occur from time to time, but all of them at once is a bit odd.
In your case I would also check DHCP leases and ports the APs are connected to. The fact that some of the APs had turned to repeater mode before the update, mean that they weren't able to receive an IP through the wired interface.
So, if I understand correctly, there is only one subnet/vlan on your network. And the APs do not seem to get an IP through DHCP. If you are not using static IPs on the APs, maybe some networking problem?
Can you connect a laptop on a port that an AP is normally connected? Does it get an IP?
Do you have Meraki switches between the MX100 and the MR32s?