Usually the VPJ control file is in the same folder as the source files. If source files are scattered in different folders, saving the VPJ will still find them.
Never move or rename source files until a project is complete. Save Project File AS routinely, giving it a unique # or name, so as not to overwrite prior saves. Using Save Project Files (no AS) will overwrite. From the HOME tab, that choice is available by clicking the chevron to the right of the Save Project button on the toolbar.