Is it possible that the packages have been restored to the wrong folder? Check that the paths in the csproj files are correct.
If they are different it could be caused by the packages now being restored to a different location. This could be caused by a NuGet.Config file being checked in specifying a node like this:
<add key="repositoryPath" value="..\..\Packages" />
The packages are being restored, by the projects are still looking at the old location.