I changed the value for GRID_FILE in user_nl_mom and noticed that ./Buildconf/mom.input_data_list still had the original value for GRID_FILE.
I think that it would be good to have the modified value appear in ./Buildconf/mom.input_data_list, so that check_input_data checks to see if the path specified in user_nl_mom exists.
I suspect that this generalizes to other files listed in ./Buildconf/mom.input_data_list.