Well, variance estimation can be obtained for two groups (for simplicity) as follows:
${\hat{\sigma}^2} = \frac{1}{2N}\sum_{i=1}^{2N}{(X_i-\mu)^2 = \frac{1}{2N}\sum_{i=1}^{N}{(X_i-\mu)^2} + \frac{1}{2N}\sum_{i=N+1}^{2N}{(X_i-\mu)^2}=\frac{1}{2}(\hat{\sigma}^2_1 + \hat{\sigma}^2_2}) = \hat{\sigma}^2$
where ${X_i}$ - is a random variable (values in your case, which are not available anymore) and ${\mu}$ - is a mean.
so, variance of the total population is average of variances for every group ${\frac{1}{2}(\hat{\sigma}^2_1 + \hat{\sigma}^2_2)}$ where ${\hat{\sigma}^2_{1}}$ is a variance of group 1, the same for group 2.
quick test on Octave, where ${x, y}$ - are two groups:
octave:1> x = 3*randn(1000, 1);
octave:2> y = 3*randn(1000, 1);
octave:3> var(x)
ans = 9.0051
octave:4> var(y)
ans = 8.8170
octave:5> 0.5*(var(x) + var(y))
ans = 8.9111
octave:6>
${\hat{\sigma}^2_{1} = 9.0051}$, ${\hat{\sigma}^2_{2} = 9.0051}$, ${\hat{\sigma}^2 = 8.9111}$
Think of your estimation as a random variable, it has it's own mean and variance.
[EDIT]
there is a better answer (and more correct).