You note first that $$\text{div}(\omega_{\epsilon}\ast u_{\epsilon})=
\omega_{\epsilon}\ast\text{div }u_{\epsilon}=0,
$$
so that, at least formally,
$$
\langle(\omega_{\epsilon}\ast u_{\epsilon})\cdot \nabla u_{\epsilon},u_{\epsilon}\rangle_{L^2}=
\langle\partial_j u_{\epsilon},
(\omega_{\epsilon}\ast u_{\epsilon})_ju_{\epsilon}\rangle_{L^2}
=-\langle u_{\epsilon},\partial_j
(\omega_{\epsilon}\ast u_{\epsilon})_ju_{\epsilon}\rangle_{L^2},
$$
and thus
$
\langle(\omega_{\epsilon}\ast u_{\epsilon})\cdot \nabla u_{\epsilon},u_{\epsilon}\rangle_{L^2}=0.
$
The sequel is standard, you multiply in $L^2$
the equation by $2u_\epsilon$ and you get by integration in time for $t\ge 0$,
$$
\Vert u_\epsilon(t)\Vert_{L^2}^2+2\int_0^t\Vert \nabla u_\epsilon(t')\Vert_{L^2}^2 dt'=\Vert u_\epsilon(0)\Vert_{L^2}^2,
$$
yielding the sought result.