Replacing li-ion cells in handheld drill battery
Only the single cell needs to be considered bad; Li-ion cells that are bad won't charge safely/properly, much less handle an actual charge. Be sure to dispose of the cell according to local safety and environmental regulations.

Provided the battery chemistry is the same (there are several different chemistries called "Li-ion") and that the cells have very similar C ratings (or even if the lower capacity battery has a proportionally higher C rating) there should be no problem using the charger for the lower capacity battery with a higher capacity battery. The charge time will simply be extended accordingly.