Currently, isolated users cannot be used to manage existing sites that have been created with the user isolation option turned off. Instead, you'll need to create a new site with user isolation enabled.
This error can occur when files under source control in the site directory have been changed by the application and will be overwritten by the new deployment.
To fix this, you should SSH into your website directory and run the following command to discard the changes:
git reset --hard && git clean -df
You should also review your application and fix any part of it that may be writing to a source controlled directory on your server. Otherwise, you may continue to get this error in subsequent deployments.