Solution
Right click on project > Clean
Right click on project > Run qmake
Right click on project > Build
Run - worked first time
Why it works
The reason this worked is because Run qmake updates your Makefile. For some reason qt is not automatically updating paths when you make changes to your project such as adding or removing files. Running qmake forces qt to update the paths for your project which enables it to find the mainwindow.obj file. You probably could just run qmake and your problem would be solved.