You can change the footprint in PCBnew itself. Just tap E keeping mouse on the footprint.
After the edit, export "Component .cmp file" from PCBnew & import it into EeSchema that'll update footprint association in schematic (similar to back annotate).
If you proceed with regular CvPcb method, do generate new netlist , read it in PCBnew & remember to check "Exchange Footprint" option to "Change" while reading netlist.