One thing worth deciding while you are rebuilding anyway: whether these should be system containers at all.
If an environment exists to run one service, an application container with its data on a dataset is simpler and survives platform changes better — you have just seen what happens when the management layer disappears.
System containers earn their place when you genuinely want a persistent machine you administer: several services, a package manager, state that is not one application's database. Worth sorting your environments into those two piles before recreating all of them the same way.