When you add the new Project Manager and you are going to upgrade a project we read the Projects.xml file and replace the bin folder, Sitefinity folder and the project file. It is better to replace backup your project file, because the project manager will override yours and you could lose some data. Please check the upgrade instructions.
"IMPORTANT: If your project is part of a larger solution where you have custom projects that reference Sitefinity assemblies, check the references to those assemblies in your project and make sure that they are referencing the newer assemblies."
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