If I want to remove a cluster from a rancher server without uninstalling all of its fleet helm deployments, would it make sense to first delete its fleet agent, then the cattle agent and only then remove it from the rancher server?

It depends on what type of cluster it is. For an imported cluster, you can delete it from Rancher but the cluster and all the deployments remain intact. For clusters where Rancher installed kubernetes and/or provisioned nodes, there is no supported path to then manage the cluster outside Rancher.

Is it possible that I deleted an imported cluster from rancher and it deleted all of my fleet deployments from within this cluster? maybe related to https://github.com/rancher/fleet/issues/263

Yes