A large C# solution has a number of subprojects. It just compiled OK. Two projects each use dlls from the other. Projects A uses B.dll and B uses A.dll. I ran Clean on the entire solution and now A cannot compile because I cannot add B.dll because B.dll (debug) does not exist, so A.dll also does not exist.
I had the same problem a bit earlier, so I saved my changed files, rechecked out the code, compiled, then added my changes and make the other appropriate changes. After a few changes, which all use a static public class I recently created, the solution compiled. And now it doesn't. And of course since many subprojects rely on A.dll they too no longer compile.