At present in my organization we take hot backups of Bamboo and use these to test upgrades.
Ideally we'd have time to stop all agents, and shutdown Bamboo before taking a cold backup. Alas, this cannot be done.
Often the agents are running when we startup the test upgrade instance, and start doing jobs we don't want them to do (as production is already running them).
Ideally we'd like a switch that can be passed via bamboo.sh to disable all agents on startup, so that when the upgraded instance is running, no jobs can run until the user starts re-enabling the agents manually.