This problem appeared for me when I was creating folders in the filesystem (not in my solution) and moved some projects around.
Turns out that the package paths are relative from the csproj files. So I had to change the "HintPath" of my references:
<Reference Include="EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089, processorArchitecture=MSIL">
<HintPath>..\packages\EntityFramework.6.1.3\lib\net45\EntityFramework.dll</HintPath>
<Private>True</Private>
</Reference>
To:
<Reference Include="EntityFramework, Version=6.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089, processorArchitecture=MSIL">
<HintPath>..\..\packages\EntityFramework.6.1.3\lib\net45\EntityFramework.dll</HintPath>
<Private>True</Private>
</Reference>
Notice the double "..\" in 'HintPath'.
I also had to change my error conditions, for example I had to change:
<Error Condition="!Exists('..\packages\Microsoft.Net.Compilers.1.1.1\build\Microsoft.Net.Compilers.props')" Text="$([System.String]::Format('$(ErrorText)', '..\packages\Microsoft.Net.Compilers.1.1.1\build\Microsoft.Net.Compilers.props'))" />
To:
<Error Condition="!Exists('..\..\packages\Microsoft.Net.Compilers.1.1.1\build\Microsoft.Net.Compilers.props')" Text="$([System.String]::Format('$(ErrorText)', '..\..\packages\Microsoft.Net.Compilers.1.1.1\build\Microsoft.Net.Compilers.props'))" />
Again, notice the double "..\".