Calling /removeNode is the right thing to do. If a machine fails in such a way where the data directories are lost, then /removeNode must be called on the existing cluster to clean up the original membership. Otherwise, it’s expected that the original instance can come back up healthy again.
A majority of the group must be up to service requests. So, with 3 Alphas in a group, at least 2 (majority of 3) must be up and running. Similarly, 2 of the 3 Zeros must be up as well. a 6-node Dgraph cluster (3 Zeros, 3 Alphas) is resilient to losing 1 Zero and/or 1 Alpha instance and the remaining cluster instances can still serve requests.