In pcb_new the footprints are really stored within the pcb file. This is not the case for eeschemas symbols.
They are cached in the so called cache lib.
If a symbol changes in the library, kicad will ask you if you want to rescue the symbol or use the symbol that is currently in the lib. (If kicad detects a change between the cached symbol and the library symbol)
This dialog should pop up as soon as you open the schematic.
But remember in kicad v4 symbol names need to be unique over all libs. Kicad will take the symbol with the specified name from the lib having the highest priority. So if you change a symbol from the official lib and safe it in your own lib, kicad might still take the other official symbol. To go around this make sure your personal lib is near the top in the component libs dialog.