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After upgrading the App-V 5.0 Service Pack 1 Database and Management Server, the following error is generated when loading the App-V management console: Could not load file or assembly 'Newtonsoft.Json, Version=4.5.0.0, Culture=neutral, PublicKeyToken=30ad4fe6b2a6aeed' or one of its dependencies. The located assembly's manifest definition does not match the assembly reference. (Exception from HRESULT: 0x80131040) To know more about resolving this issue click on the below official Microsoft TechNet link: http://blogs.technet.com/b/appv/archive/2015/10/22/app-v-5-1-support-tip-management-console-generates-could-not-load-file-or-assembly-newtonsoft-json-error.aspx

After upgrading App-V 5.0 Management and Publishing servers to App-V 5.1, you may encounter a problem where publishing no longer function properly and the following issues appear: - Accessing the Publishing URL in Internet Explorer from directly on the Publishing Server (e.g.http://localhost:82, where 82 is the port assigned to the Publishing Server Service) generates the following error message: The website cannot display the page - The event below is seen in Event Viewer\Applications and Servers logs\App-V\Server-Publishing-Private\Debug: Failed to pre-load publishing metadata.  Message: Object reference not set to an instance of an object.  Details:   Stack Trace:     at Microsoft.AppV.Server.Publishing.PublishingMetadataSerializer.PackageSerializer.Load(XElement pkgElement, PublishingMetadata& data)     at Microsoft.AppV.Server.Publishing.PublishingMetadataSerializer.RootSerializer.Load(XmlReader reader)     at Microsof...

Check out  Simon Dettling  post about how to upgrade your App-V management server to 5.1 in easy steps. http://msitproblog.com/2015/10/18/upgrade-your-app-v-management-server-to-5-1/ Also check Microsoft Technet link. http://blogs.technet.com/b/appv/archive/2015/09/23/a-simplified-microsoft-app-v-5-1-management-server-upgrade-procedure.aspx

Check this official Microsoft Technet Link to know more about how to upgrade App-V 5.1 Management Server http://blogs.technet.com/b/appv/archive/2015/09/23/a-simplified-microsoft-app-v-5-1-management-server-upgrade-procedure.aspx