I have a couple of projects which reference SQL Server assemblies. With SQL Server 2005 and SQL Server 2008 I am currently maintaining 2 project files which point to the same so
Searching for a solution to the same problem you had I came to the proposed solution of having a Condition on the ItemGroup. But this had a side effect because in Visual Studio references I could see both references, which also impacted ReSharper.
I finally use a Choose When Otherwise and I don't have any issue anymore with ReSharper and Visual Studio showing two References.
{A7714633-66D7-4099-A255-5A911DB7BED8}
app.Controls %28Sources\client1\app.Controls%29
{2E6D4065-E042-44B9-A569-FA1C36F1BDCE}
app.Controls %28Sources\app.Controls%29