We analyze the effect of pairing on particle transport in time-dependent theories based on the Hartree-Fock-Bogoliubov (HFB) or BCS approximations. The equations of motion for the HFB density matrices are unique and the theory respects the usual conservation laws defined by commutators of the conserved quantity with the Hamiltonian. In contrast, the theories based on the BCS approximation are more problematic. In the usual formulation of TDHF+BCS, the equation of continuity is violated and one sees unphysical oscillations in particle densities. This can be ameliorated by freezing the occupation numbers during the evolution in TDHF+BCS, but there are other problems with the BCS that make it doubtful for reaction dynamics. We also compare different numerical implementations of the time-dependent HFB equations. The equations of motion for the $U$ and $V$ Bogoliubov transformations are not unique, but it appears that the usual formulation is also the most efficient. Finally, we compare the time-dependent HFB solutions with numerically exact solutions of the two-particle Schrodinger equation. Depending on the treatment of the initial state, the HFB dynamics produces a particle emission rate at short times similar to that of the Schrodinger equation. At long times, the total particle emission can be quite different, due to inherent mean-field approximation of the HFB theory.