Battery School

The reason it is not advisable to mix batteries (actually they are cells) of different capacities or charge states is that when connected in series some batteries will discharge before others.  When this happens, the discharged batteries will be subjected to reverse polarity which will likely damage them.  Also, during charging a series string of batteries the lower capacity ones will reach full charge before the higher capacity ones which can cause them to overheat and be damaged.

Modern Lithium-Ion batteries with multiple series cells are properly managed by electronic circuits which monitor the voltage of each cell during charge and discharge to prevent such problems.

Neil