What does annihilation of charges mean? Say you had two (parallel plate) capacitors that were initially charged to unequal charges. If you connect these capacitors in parallel such that the positive terminal of one plate is connected to the negative terminal of the other, what exactly happens to the total charge of the two capacitors? I read somewhere that the charges "annihilate" each other due to the wrong connection and the total charge of the system reduces, but what does that mean exactly? How do charges annihilate each other, and where do they go?
Also if the charge of the system reduces, there must be a consequent decrease in the potential difference between the plates of each of the capacitors. What if this was forcibly maintained by an external battery? What would happen to the charges then?
 A: 
I read somewhere that the charges "annihilate" each other due to the wrong connection and the total charge of the system reduces,

"Annihilate" is a bad terminology to use for classical electrodynamics, that can model capacitors and circuit elements. It is a term used in particle physics, when a particle meets an antiparticle and both are annihilated, and the total quantum numbers add up to zero.
For the macroscopic case of  the capacitors you are describing it means that charge is neutralized . What produces the charge in a capacitor? The potential difference draws  electrons to one plate  creating an excess of negative charge, leaving the atoms on the other plate  positive. With the connections you suggest, part of the electrons will go  and neutralize  part of the positive charge, (make part of the atoms neutral again) so that  the charges would be balanced and lower.

Also if the charge of the system reduces, there must be a consequent decrease in the potential difference between the plates of each of the capacitors. What if this was forcibly maintained by an external battery? What would happen to the charges then?

You will have a circuit with two parallel capacitors, maintained by a battery at a certain charge.
