BizTalk Server is designed to allow for an easy upgrade experience from previous versions. The BizTalk Server 2013 and 2013 R2 Upgrade Guide is available at Installation Guides Related to BizTalk Server 2013.
The compressed file of schemas will be replaced when an upgrade is performed. If you upgrade Microsoft BizTalk Server to a later build (for example, from a beta version to the retail release version), the MicrosoftEdiXSDTemplates.exe file in your installation will be replaced with the MicrosoftEdiXSDTemplates.exe file associated with the upgrade. If you plan to continue to use the schemas from the old compressed file, you will no longer have access to the compressed file after the upgrade unless you back up the old compressed file. For more information, see Install EDI schemas at Post-configuration steps to optimize your environment.