Altium footprint manager
I've had issues like this myself, it had something to do with Altium forgetting to load the library, double check to see if the library you're updating from is still installed, I'd had the library open, I edited a part and then when I went to update the PCB it couldn't find the footprint, I checked and the library was no longer installed, re-adding the library fixed the issue. But it seems odd that you can update the schematic though.