Is anyone else seeing Ninja RMM agents go offline on domain controllers after an update?

Check whether the agent is actually crashing on the server, rather than treating every offline status as the same problem. Windows event logs may show agent crashes, and crash dumps may be under C:\Windows\SysWOW64\config\systemprofile\AppData\Local\CrashDumps.

A reboot restored one affected server, while another needed an agent reinstall. If you can reach a server through an authorized onsite workstation, compare its agent version and logs with a working machine before changing anything.

There may also be a service-side issue. Some devices have appeared online in the device list but offline when opened, and the status later returned to normal. Others reported no trouble at all, so this doesn't look uniform across every environment.

Try opening the device from its organization page to see whether remote access is available there. That won't necessarily help if the device itself is marked offline, but it's a quick check.

Check the installed agent version if you can get onto the server another way. Updating the agent helped in one case, and a manual reinstall helped on a server with a much older version. Test on one machine first rather than removing agents across all the affected controllers.

For the immediate work, an authorized RDP connection from an accessible onsite computer may be a workaround if RDP is already enabled and permitted. The RMM remote options can disappear when it thinks the server is offline, even though another route to the server may still work.

I wouldn't assume the update is the cause just from the timing. There were also reports of an upstream infrastructure issue around the same time, while some servers had agent crash events. Check the vendor's service notices and the local logs separately.

Also, staging your own configuration changes is useful, but it may not give you control over when a hosted RMM provider rolls out its service updates.