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Customized area definitions, derived by cloning the SPS or other area folders as described in KB 898631, could fail to upgrade. Described here, is the work around to achieve a successful content upgrade.
The upgrade process will fail and the upgrade logs will reflect "/Pages" cannot be found messages. In some cases, the upgrade might appear to complete, but when attempting to access the upgraded portal site e.g. the system will redirect to resulting in a 404 File Not Found error instead of the proper page.
The cause of the upgrade failure is due to the cloning of the area template as described in KB 898631. During the cloning process, a new area ID is given to the definition. Naturally, the upgrade engine does not have awareness to or knowledge of any custom definitions. As a result, it may attempt to upgrade the areas anyway based on the standard definitions, but customization may cause unexpected errors to occur during the upgrade.
Remember to always conduct full backups prior to attempting this procedure. It is preferable to restore said backups to separate TEST servers for conducting the upgrade test. NEVER use production servers as a proving ground.
To resolve the issue, the portal areas that have custom definitions, must be reverted back to base definitions by following these steps:
Navigate to the home page.
In the "Actions" section of the left hand vertical menu, click "Change Settings".
On the "Change Settings" page, click the "Page" tab at the top.
In the "Subarea Templates" section, ensure the "All subareas will use the following template" radio button option is selected.
In the dropdown below, select the "SharePoint Portal Server Site" template.
Click the "OK" button.
Your areas should now be based on the standard base template which should allow the upgrade process to complete successfully. You can verify this by navigating to these areas. You should notice a definite (depending on your level of customization) visual difference in the pages. Customization will have to be reapplied once the upgrade was completed, so plan additional time for this as well.