Oh well I found it, might as well answer it myself as well.. There should be a .vbproj file on your application directory, for VB.NET, I'm sure other languages have it different. But you have to edit this, whether you deleted your extra .resx or not:
<EmbeddedResource Include="yourMmainForm.resx">
<DependentUpon>yourMainForm.vb</DependentUpon>
</EmbeddedResource>
In my case Designer.resx was already dependent upon my Main form so even after I deleted the file the duplicate was still there, ok now it's fixed.