Altium - Changing the libraries for completed schematics and PCB design
You can remove All.SchLib and All.PcbLib from your project any time you want without affecting the schematics or layout files. Even if you haven't created the ProjectA.Schlib and ProjectA.Pcblib files first.

You could even do that and then rebuild the parts of the libraries you used with the "make library from design" commands afterwards.