Can no longer build MG 3.5 for desktop after installing MG 3.6

I installed MonoGame 3.6 on my system (without uninstalling MonoGame 3.5 or anything) and projects I had set to build with MonoGame 3.5 stopped compiling with the following warning:

Severity	Code	Description	Project	File	Line	Suppression State
Warning		There was a mismatch between the processor architecture of the project being built "MSIL" and the processor architecture, "x86", of the implementation file "C:\Program Files (x86)\MonoGame\v3.0\Assemblies\WindowsPhone\x86\SharpDX.WP8.dll" for "C:\Program Files (x86)\MonoGame\v3.0\Assemblies\WindowsPhone\x86\SharpDX.WP8.winmd". This mismatch may cause runtime failures. Please consider changing the targeted processor architecture of your project through the Configuration Manager so as to align the processor architectures between your project and implementation file, or choose a winmd file with an implementation file that has a processor architecture which matches the targeted processor architecture of your project.	DataTypes			

Now here’s the weird part: my project isn’t even supposed to build for WindowsPhone… It was supposed to be a desktop application.

So I opened references and I noticed that all the MonoGame 3.5 assemblies are missing, except for the ones for WindowsPhone, which is probably why its trying to use it.

Can’t I have both MG 3.5 and 3.6 on the same computer? Is this a bug in the installer or by-design?