> you pretty well just can't, without risk of deleting everything

This is one hyper annoying area.

It is possible to get around it, but it's ugly, drop to L1 and override logical id:

   let vpc = new ec2.Vpc(this, 'vpc', { natGateways: 1 })
   let cfnVpc = vpc.node.defaultChild as ec2.CfnVPC
   cfnVpc.overrideLogicalId('MainVpc')

You have to do this literally for every resource that's refactored.

For us, we run 2 stacks. One that basically cannot/should-not be deleted/refactored. VPC, RDS, critical S3 buckets - i.e. critical data.

The 2nd stack runs the software and all those resources can be destroyed, moved whatever w/o any data loss.