Suppose we are given a vector field $\mathbf{F} \colon \mathbb{R}^4 \to \mathbb{R}^3$ that evolves with time and describes the way, say, liquid particles move in a tank. Also, we are given a parametric surface $\mathscr{S}$ that is parameterized by
$$\mathbf{r}(u, v, t) = x(u, v, t)\mathbf{i} + y(u, v, t)\mathbf{j} + z(u, v, t)\mathbf{k}.$$
(Note that the surfaces evolves with time too; it "moves".) Moreover, let the (spatial) domain of $\mathbf{r}$ be $A$.
Now the question I want to be able to answer is: how to compute flux through an area element taking motion of both the surface and the vector field into account?
See what I tried:
(1) First I need to compute the unit normal to the surface at a particular instant:
$$\mathbf{\hat{N}}(u, v, t) = \frac{\frac{\partial}{\partial u}\mathbf{r}(u, v, t) \times \frac{\partial}{\partial v}\mathbf{r}(u, v, t)}{\Big| \frac{\partial}{\partial u}\mathbf{r}(u, v, t) \times \frac{\partial}{\partial v}\mathbf{r}(u, v, t)\Big|}.$$
(2) Taking motion into account, we have that the surface element at time $t$ passes the space at rate $$\Big\langle \mathbf{\hat{N}}(u, v, t), \frac{\partial}{\partial t}\mathbf{r}(u, v, t) \Big\rangle.$$
(3) Now all we do at each area element is to take the difference of the two vectors: one vector from the vector field and the other one is from the motion of the surface. For example, if at some instant an area element moves with the same speed and direction as the vector implied by the vector field, the flux should be zero. Putting all together, I have the following:
$$ \begin{align} \Phi(t) &= \iint_{\mathscr{S}} \Bigg\langle \mathbf{F}, \mathbf{\hat{N}}\Bigg\rangle - \Bigg\langle \frac{\partial}{\partial t}\mathbf{r}, \mathbf{\hat{N}}\Bigg\rangle\, \mathrm{d}S \\ &= \iint_{\mathscr{S}} \Bigg\langle \mathbf{F} - \frac{\partial}{\partial t}\mathbf{r}, \mathbf{\hat{N}} \Bigg\rangle\, \mathrm{d}S \\ &= \iint_{A} \Bigg\langle \mathbf{F} - \frac{\partial}{\partial t}\mathbf{r}, \mathbf{\hat{N}} \Bigg\rangle \Bigg| \frac{\partial}{\partial u}\mathbf{r} \times \frac{\partial}{\partial v}\mathbf{r} \Bigg| \, \mathrm{d}u \, \mathrm{d}v \\ &= \iint_{A} \Bigg\langle \mathbf{F}(\mathbf{r}(u, v, t), t) - \frac{\partial}{\partial t} \mathbf{r}(u, v, t), \frac{\partial}{\partial u} \mathbf{r}(u, v, t) \times \frac{\partial}{\partial v}\mathbf{r}(u, v, t) \Bigg\rangle \, \mathrm{d}u \, \mathrm{d}v. \end{align} $$
Is the above calculation correct? If yes, than the volume through the surface $\mathscr{S}$ within time range $[a, b]$ is simply $\int_a^b \Phi(t) \, \mathrm{d}t$?
Yes, this the calculation is correct. In a constant density setting (such as a liquid), the flux you calculate is the (signed) amount of stuff that goes through the surface in an infinitesimal time interval.
Physical intuition dictates that these things must happen:
And indeed, these hold true. When doing such "physical calculus problems", I strongly suggest making sure that the solution exhibits physically correct behavior.
I did not only check these criteria. I also went through your reasoning, and you have explained your solution well.
Additional remarks: