References removed from packages.config during 'update-package -reinstall'

After cloning a smallish repo(2 projects) I went to update the packages in project B and it removed all the lines in packages.config because they already exist in a folder under project A.

The PM console reads like:

Removed package 'Microsoft.PackageA' from 'packages.config'

Successfully uninstalled 'Microsoft.PackageA' from Myproject.business

Package 'Microsoft.PackageA' already exists in folder 'C:\Myproject\packages'

update-package : Failed to add reference to 'PackageA'.
  Error HRESULT E_FAIL has been returned from a call to a COM component.
At line:1 char:1
+ update-package -reinstall
+ ~~~~~~~~~~~~~~~~~~~~~~~~~
    + CategoryInfo          : NotSpecified: (:) [Update-Package], Exception
    + FullyQualifiedErrorId : NuGetCmdletUnhandledException,NuGet.PackageManagement.PowerShellCmdlets.UpdatePackageCommand