Build with msbuild and dynamically set project references
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.
<Choose>
<When Condition=" '$(Configuration)' == 'client1DeployClickOnce' ">
<ItemGroup>
<ProjectReferenceInclude="..\client1\app.Controls\app.Controls.csproj">
<Project>{A7714633-66D7-4099-A255-5A911DB7BED8}</Project>
<Name>app.Controls %28Sources\client1\app.Controls%29</Name>
</ProjectReference>
</ItemGroup>
</When>
<Otherwise>
<ItemGroup>
<ProjectReference Include="..\app.Controls\app.Controls.csproj">
<Project>{2E6D4065-E042-44B9-A569-FA1C36F1BDCE}</Project>
<Name>app.Controls %28Sources\app.Controls%29</Name>
</ProjectReference>
</ItemGroup>
</Otherwise>
</Choose>
Every MSBuild element (ok almost every) can have a Condition associated with it. What I would suggest is that you edit the project file (which is an MSBuild file itself) and place all the SQL server references in an ItemGroup which has a condition on it for instance:
<ItemGroup Condition="'$(SqlServerTargetEdition)'=='2005'">
<!-- SQL Server 2005 References here -->
<Reference Include="..."/>
</ItemGroup>
And another ItemGroup for Sql server 2008:
<ItemGroup Condition="'$(SqlServerTargetEdition)'=='2008'">
<!-- SQL Server 2008 References here -->
<Reference Include="..."/>
</ItemGroup>
You should provide a default value for the property SqlServerTargetEdition before those items are declared. Then at the command line you can override that value using the /p switch when invoking msbuild.exe.
Sayed Ibrahim Hashimi
My Book: Inside the Microsoft Build Engine : Using MSBuild and Team Foundation Build