Upgrading Commerce Server 2009 deployment on WSS to MOSS
If you have deployed any of the Commerce Server 2009 sample sites or your own custom site on a Windows SharePoint Services 3.0 based deployment, and then decide to upgrade that deployment to Office SharePoint Server 2007, your Commerce sites already deployed will cease to function correctly.
This is because when you use the SharePoint Commerce Services Configuration Wizard to deploy the site, it will check to see if WSS or MOSS is deployed and based on what is deployed it will choose the appropriate WSP files to deploy for the site collection. There are different versions for WSS and MOSS.
If you wish to upgrade an existing WSS deployment to MOSS you will need to back-up all of your site databases and site content, then remove the site in SharePoint Central Administration prior to performing the upgrade. Once the upgrade is complete you can deploy the appropriate site using the SharePoint Commerce Services Configuration Wizard and then merge any site customizations previously done into the new site.