environment variables removed in config.yml after running theme new

[tommypepsi]

Describe the bug We recently added the creation of a backup in our github actions using the theme new command. When doing theme new --env=backup ...other_settings it removes environment variables from the config.yml file.

To Reproduce Steps to reproduce the behavior:

1. in the config.yml file add a development environment with an environment variable for the theme_id. ex: theme_id: ${DEV_THEME_ID}
2. run theme new --env=backup --password=mypassword --store=store.myshopify.com --name=theme
3. theme_id will be removed from the development environment in config.yml.

Expected behavior The environment variables should stay present in the config.yml after runing theme new

Environment (please complete the following information):

• OS [e.g. iOS]: windows 10
• Themekit version (run theme version to check): 1.1.4
• Editor [e.g. atom, sublime]: vs code