My team recently needed to update from TFS 2012 Update 1 to TFS 2012 Update 4, but ran into a problem during the upgrade:

Looking closer at the log file, it had this information:

XML parsing failed at line 1, column 0: A document must contain exactly one root element.
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Errors in the metadata manager. An error occurred when instantiating a metadata object from the file, ‘\\?\d:\Program Files\Microsoft SQL Server\MSAS11.MSSQLSERVER\OLAP\Data\Tfs_Analysis.0.db\Team System.8676.cub.xml’.

[Info @22:20:14.393] Microsoft.AnalysisServices.OperationException: XML parsing failed at line 1, column 0: A document must contain exactly one root element.
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Errors in the metadata manager. An error occurred when instantiating a metadata object from the file, ‘\\?\d:\Program Files\Microsoft SQL Server\MSAS11.MSSQLSERVER\OLAP\Data\Tfs_Analysis.0.db\Team System.8676.cub.xml’.

To get around this we:

1. Restored the TFS_Configuration and TFS_[Collections] databases to their pre-upgrade state
2. Re-ran the upgrade wizard, but this time unchecked the Reporting portion of the upgrade. This causes the installer to ignore the warehouse and analysis services part of the install
3. After the install completed, we deleted the tfs_warehouse and tfs_analysis databases
4. Following instructions from this TFS Setup Support blog post, rebuilt the warehouse and analysis databases

Upgrade complete!