Restore original iTunes library after system format

I am using an Apple Music account with Apple Music Version 1.0.1.37 (new iTunes) to sync my physical music collection across multiple computers and portable devices. The main computer is at home and I'm keen to wipe it and start over but want to make sure I can reestablish it as the original music source for Apple Music once I have formatted the old system, reinstalled a fresh OS and copied the files back into iTunes/Apple Music – assume here I will need to drop them back into Apple Music and popular the music folder that way but what will happen then? Will iTunes just rewrite those files with files from the cloud or will the cloud check the physical library against itself and recognise it as what was there before if it is exactly the same? To explain my reasons, a lot of the music is lossless and the files in the cloud have been re-encoded I am keen to keep my full qual music on main system for the home sound system.

Thanks in advance.