We use inelastic neutron scattering to study the evolution of the generalized phonon density of states (GDOS) of the $n$-type high-$T_c$ superconductor Nd$_{2-x}$Ce$_x$CuO$_{4+delta}$ (NCCO), from the half-filled Mott-insulator ($x=0$) to the $T_c=24$ K superconductor ($x=0.15$). Upon doping the CuO$_2$ planes in Nd$_2$CuO$_{4+delta}$ (NCO) with electrons by Ce substitution, the most significant change in the GDOS is the softening of the highest phonon branches associated with the Cu-O bond stretching and out-of-plane oxygen vibration modes. However, the softening occurs within the first few percent of Ce-doping and is not related to the electron doping induced nonsuperconducting-superconducting transition (NST) at $xapprox 0.12$. These results suggest that the electron-lattice coupling in the $n$-type high-$T_c$ superconductors is different from that in the $p$-type materials.