I had the same problem once..
though since I use Git I could simply reclone the project and barely lost anything
was also a bit shocked, I m new to monogame and experimented with the content pipeline, accidently added an already exiting file from another folder to the content pipeline...
it made a reference to that other folder, I deleted it and the whole project was gone^^
(didnt see that "exclude" was also an option and thought delete would do the same^^)