If you have 3 main (please avoid using master, ) control plane nodes you should be fine replacing 1 at a time. The only thing is that your cluster will not be able to make any decisions/schedule any new workload, but the existing workloads will run fine.
The recommendation of 5 main nodes is based on the fact that you will always have a majority to reach quorum on the state decisions for etcd even if one node goes down. So if you have 5 nodes and one of them goes down you will still be able to schedule/run workloads.
In other words:
3 main nodes
- Can tolerate a failure of one node.
- Will not be able to make decisions
5 main nodes
- Can tolerate a failure of one node.
- Can still make decisions because there are 4 nodes still available.
- If 2 failures happen then it's tolerated but there is no quorum.
To summarize, Raft which is the consensus protocol for etcd tolerates up to (N-1)/2 failures and requires a majority or quorum of (N/2)+1. The recommended procedure is to update the nodes one at a time: bring one node down, and then a bring another one up, and wait for it to join the cluster (all control plane components)