Yhe schematic should always be the controlling document, and always control the PCB parts and conectivity, except for the following caveats, where back annotation from the PCb to Schematic is allowed:
Gate and pin swaps, to improve routability - performed on the PCB and back annotated immediatly to the schematic.
Attributes and metadata create by any high speed routing package, back annotate as above.
In ALL other cases, change the schematic and ECO to the layout.
Follow a strict regime when applying this, it will save problems in the future.
The schematic and PCB should always match each other, when the PCB is released for manufacture.