Recently we did a MS CRM 2013 upgrade from MS CRM 4.0 for one of our customer and during the installation of MS CRM 2013 UR 2 we got this error. We tried to look if someone has faced this issue before and found this thread (thanks to poster) ,in Microsoft Dynamics forum, although it is an unsupported changes but it helped us to resolve this issue. We followed below steps which are mentioned there and it resolved our issue.
1. Took a complete backup of your MSCRM_CONFIG database
2. Rename dbo.dbupdateinstallinfo to dbo.dbupdateinstallinfo-old, under mscrm_config db.
3. Rename dbo.dbupdateinstallinfo_V5 to dbo.dbupdateinstallinfo_V5-old under mscrm_Config db.
4. Installed MS CRM UR 2.
MS CRM 2013 UR 2 recreated these tables as per a new installation of CRM 2013.
Hope it will help someone!!
Thank you for this post. It helped applying CRM 2013 SP1 to a CRM 2013 deployment upgraded from CRM 4.