I'll assume when you mention these "new footprints" you mean they have a new JEDEC_TYPE name? If so, that's ok to:
1) Export a placement file from the current board
2) Import a new netlist (that might remove parts that have been renamed
3) Import the placement file (old placement). This will replace only the parts awaiting placement
4) Finally? Run Tools/Derive Connectivity - this should connect what might be been unconnected.