Parametrize S(t) as \mathbf{x}(s_1,s_2,t) for (s_1,s_2) \in \Omega \subset \mathbb{R}^2. Then <br />
\frac{d}{dt} \int_{S(t)} \mathbf{F} \cdot d\mathbf{S} = \frac{d}{dt} \int_{\Omega} \mathbf{F} \cdot \mathbf{n}\,ds_1\,ds_2. Now \Omega is independent of t so we can pull the derivative inside the integral, but it becomes a partial derivative at fixed s = (s_1,s_2). We then have <br />
\left(\frac{\partial\mathbf{F}}{\partial t}\right)_{s} = \left(\frac{\partial\mathbf{F}}{\partial t}\right)_{\mathbf{x}} + (\mathbf{u} \cdot \nabla) \mathbf{F}. We also have <br />
\begin{split}<br />
\left(\frac{\partial n_i}{\partial t}\right)_s &= \epsilon_{ijk} \frac{\partial}{\partial t} \left( \frac{\partial x_j}{\partial s_1}\frac{\partial x_k}{\partial s_2}\right) \\<br />
&= \epsilon_{ijk} \left(\frac{\partial u_j}{\partial s_1} \frac{\partial x_k}{\partial s_2} + \frac{\partial u_k}{\partial s_2} \frac{\partial x_j}{\partial s_1}\right) \\<br />
&= \epsilon_{ijk} \left(\frac{\partial u_j}{\partial s_1} \frac{\partial x_k}{\partial s_2} - \frac{\partial u_j}{\partial s_2} \frac{\partial x_k}{\partial s_1}\right) \\<br />
&= \epsilon_{ijk} \frac{\partial u_j}{\partial x_l}\left(\frac{\partial x_l}{\partial s_1} \frac{\partial x_k}{\partial s_2} - \frac{\partial x_l}{\partial s_2} \frac{\partial x_k}{\partial s_1}\right) \\<br />
&= \epsilon_{ijk} \frac{\partial u_j}{\partial x_l} \left(\delta_{lp}\delta_{kq} - \delta_{lq}\delta_{kp}\right)\frac{\partial x_p}{\partial s_1} \frac{\partial x_q}{\partial x_2} \\<br />
&= \epsilon_{ijk} \frac{\partial u_j}{\partial x_l} \epsilon_{lkm}\epsilon_{mpq} \frac{\partial x_p}{\partial s_1} \frac{\partial x_q}{\partial x_2} \\<br />
&= -\epsilon_{ijk} \epsilon_{klm} \frac{\partial u_j}{\partial x_l} n_m \\<br />
&= \left(\delta_{im}\delta_{jl} - \delta_{il}\delta_{jm}\right) \frac{\partial u_j}{\partial x_l} n_m\\<br />
&= n_i\frac{\partial u_j}{\partial x_j} - n_j \frac{\partial u_j}{\partial x_i}.<br />
\end{split} Hence <br />
\left(\frac{\partial}{\partial t} (\mathbf{F} \cdot \mathbf{n}) \right)_s = \left(\frac{\partial \mathbf{F}}{\partial t}\right)_{\mathbf{x}} \cdot \mathbf{n} + \mathbf{n} \cdot \left(((\mathbf{u} \cdot \nabla)\mathbf{F}) +<br />
\mathbf{F} (\nabla \cdot \mathbf{u}) - (\mathbf{F} \cdot \nabla)\mathbf{u}\right). I think the last three terms can be rearranged into -\mathbf{n} \cdot (\nabla \times(\mathbf{u} \times \mathbf{F})) on the assumption that \nabla \cdot \mathbf{F} = 0.