I managed to fix the errors by deleting the following files in %localappdata%\vcpkg:

vcpkg.user.props
vcpkg.user.targets

It seems MSVS was allowing vcpkg to import custom properties with the following

  <Import Condition="Exists('C:\Scripts\vcpkg\scripts\buildsystems\msbuild\vcpkg.targets') and '$(VCPkgLocalAppDataDisabled)' == ''" Project="C:\Scripts\vcpkg\scripts\buildsystems\msbuild\vcpkg.targets" />