I have the same issue being reported here. My unifi controller (v5.6.37) could not connect with the AP's (v3.9.27.8537) or the other way around once the unifi docker controller was updated. This happened several times in the last few weeks, every time the unifi docker was updated. The unifi docker was set to bridged network mode.
The AP's were set via set-inform to a FQDN; "htttp://xxxx.xxxxx.xx:8080/inform". Which is reachable and works to adapt new remote AP's. I currently don't have AP's on a remote site running. But I have tested it a week ago since I plan to help out and manage remote sites running Ubiquiti hardware.
Once the unifi docker was updated yesterday, I verified the set-inform address configured on the AP's using command "info". For some reason it was set to the docker's NAT'ed IP 172.17.0.5 instead of the previously set FQDN. There is no DNS entry called unifi pointing towards IP 172.17.0.5, so the setting must have come from the unifi controller at some point in time.
I read in this thread that the bridged IP doesn't work well, so I switched to custom. I set it to 192.168.123.3 in the 192.168.123.0/24 range of my UnRaid server (IP 192.168.123.10). Once set and the unfi docker came online, the AP's were all connected. So, that works like a charm.
Curious though I verified the set-inform address again on the AP's. It seems it is set to the new IP; "http://192.168.123.3:8080/inform". It seems that the controller changes the set-inform on at least local hardware. I currently don't have remote AP's online, so I don't know that it will do with those. Inside the unifi controller, the setting "hostname/ip" is set to the FQDN address and not to the old or new IP. The Ubiquiti cloud connect feature also works after the IP change without any issues.
The AP's are all UAP-AC-Lite's. No other hardware is connected at this point. I have another 3x AP's configured, which will be installed in the next couple days on a remote site. I will have to test them again before deploying them and I'm curious what a future controller update will do to them. I will keep you posted when I have any relevant information.