The solutions manual tells me that equilibrium means the voltages balancing. This doesn't make sense to me
"Equilibrium" means "steady state": all circuit parameters are constant, which means voltage and current are constant. This does not necessarily mean current or voltage are zero, but they all have to be constant.
So what is "equilibrium" in the case of your circuit?
All three components are the same, so current through them is the same.
If V1 is not equal to V2, current i will flow in resistor R, and thus in the capacitors:
\$ i = \frac{V1-V2}{R} = C_1 \frac{-dv_1}{dt} = C_2 \frac{dv_2}{dt} \$
So the capacitor with higher voltage will discharge into the capacitor with lower voltage.
If current flows in a capacitor, its voltage will change. Thus, if current is not zero, equilibrium has not been reached yet. Thus, in this circuit's case, equilibrium means current is zero, and therefore V1=V2.
Another way to say it is: at equilibrium, everything is constant so derivatives are zero, thus \$ \frac{dv}{dt} = 0 \$ thus i=0.
For any circuit with capacitors, "equilibrium" means current through the capacitors is zero. Otherwise voltage across the caps is changing, thus it's not equilibrium.
About conservation of charge:
Capacitors are insulating, so while current can flow through them, charges (in this case electrons) cannot pass. Thus your circuit is split in two halves (red and blue) and the charge in each is constant. Thus \$ Q_1+Q_2 = Constant \$.