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To upgrade Nintex Drawloop you only need to update the package via the Nintex Drawloop listing on the Salesforce AppExchange. All of your existing document packages will be kept after updating.
For detailed instructions on how to update Nintex Drawloop, you can check out our Install the app documentation. Note: when updating Nintex Drawloop you will want to select "Install for all users" during the installation process.
Nintex Drawloop Product Manager