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In my specific case this was actually caused by simply changing what labels a clusterGroup matched to. Any clusters that were no longer part of the cluster group had their bundle/apps removed.

Wouldn't keepResources have prevented that?

Looking it over, it does look like

keepResources

might work. I'll need to do some testing. I'm not the primary operator on fleet, so I am learning as I go and try to improve things along the way.