I had the same issue, my topic: http://community.monogame.net/t/cant-load-pipeline-files-with-v3-5/
First, try this steps: Upgrading to MonoGame 3.5
If it doesn’t work, try to do what I did. I created a new MonoGame 3.5 Project and I moved the entire project files to there. I choose the MonoGame Cross Platform Desktop Project, but you can use the MonoGame Windows Project, you just need ensure that the bug doesn’t happen on the new project before moving everything.