I have also reproduced this issue using the following steps
1) Bootstrap a manual environment
2) Deploy a charm that fails to complete deployment
3) Reboot local machine to ensure all connections to env are closed
4) Open terminal
5) juju switch
6) juju destroy-environment -e manual
System requests password to local ssh keyfile and attempt to destroy env, but fails
After that destroy says the environment returns that it is not bootstrapped but bootstrap returns that the machine is already provisioned.
I have also reproduced this issue using the following steps
1) Bootstrap a manual environment
2) Deploy a charm that fails to complete deployment
3) Reboot local machine to ensure all connections to env are closed
4) Open terminal
5) juju switch
6) juju destroy-environment -e manual
System requests password to local ssh keyfile and attempt to destroy env, but fails
After that destroy says the environment returns that it is not bootstrapped but bootstrap returns that the machine is already provisioned.