I am in the beginning of Mission 11 Return to the Cathedral and find myself out of fire arrows and flash bombs after dealing with 3 Hammer Haunts, 1 Hammer Spirit, and 3 Zombies. Since this is still early in the mission, do you guys think I should restart or continue? If there are any more of these undead creatures I will not have any means to kill them (unless they can be killed with a sword, which I am sure zombies can't).
Hammer Haunts can be killed with a sword. At least, it's possible to sneak up on them and kill them with a backstab. I'm not sure if you can kill them in a straight-up fight, but I think you can.
It's possible to be very sneaky in this level and hardly have to fight the zombies and haunts at all. When I first played I would freak out and try to kill every zombie but later realized that I can sneak past them in most cases. So it is possible to finish the level without flash bombs or fire arrows.
Having said that, it might be safer to restart and use them more sparingly while getting the Eye. That way you'll still have a few for emergencies later in the mission. Try being more sneaky and only fight if you're discovered. Also, in the case of Hammer Haunts, you can sneak up on them and backstab them.