Once the following steps are done

toolkit.apply_permissions_to_backup_groups()
toolkit.replace_workspace_groups_with_account_groups()

but not the last:
toolkit.apply_permissions_to_account_groups()

it is not possible to re-run the tool since the tool cannot build the state anymore.

A simple fix would be to re-construct the state based on backup groups before running toolkit.apply_permissions_to_account_groups()