Yeah, dealing with agent issues sucked; I'm glad I haven't worked on one of those setups in awhile. And if the agent bootstrapped some part of the shell-in-and-remotely-troubleshoot tooling, good luck debugging it, and if the agent bootstrapped the telemetry system, good luck telling the difference between "host with agent failure" and "host that disappeared"... anyway. Fun times.
For hour+ runtimes I really do think that's pretty much always user error. I know that's a clichéd and grouchy comment, but (as, I'll admit, a Puppet fan with some personal defensiveness for a favored tool) I do think it's true in this case.
Also, for bigger inventories on a single vm runtimes shot up quickly in the hour realm