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In Microsoft Office SharePoint Server 2007, if you use the SPFolder.MoveTo method to move items and move folders between document libraries, an incremental crawl does not obtain the moved items and the moved folders.
To resolve this problem, apply both of the following hotfixes:
973409 Description of the Office SharePoint Server 2007 Cumulative Update Server Hotfix Package (Coreserver.msp): August 25, 2009
973410 Description of the Windows SharePoint Services 3.0 Cumulative Update Server Hotfix Package (Sts.msp): August 25, 2009