Can you clarify what files are updated/created when pushing to Flywheel?
Is it a total rewrite of the live site replacing plugins/themes/users etc. or are just the settings updated on plugins and themes that already exist on the live site?
Are users created or destroyed if they are on the local site and not the live site?
All non-WordPress core files are pushed/pulled. This means any files in wp-content as well as files in the root of the site that aren’t wp-includes, wp-admin, wp-config.php, etc.
When you push from local up to a live site does it overwrite media uploads on the live site? Could you lose media items on the live site if they are not in your local version?