How to Persist a Windows Azure Pack Theme after Microsoft Upgrade
Applies To: Windows Azure Pack
When running Microsoft Upgrade the Content folder is refreshed and the Custom theme and custom extensions may be deleted. To persist any changes made to this folder, Create a folder called app_customTheme under \inetpub\MgmtSvc-TenantSite and in it maintain a copy of all changes made to the Content folder. This includes any changes to the theme, Adding Custom Extensions, Modifying existing extensions.
You should do this on every management portal for tenants you have customizations on.