Hello. I replaced a hot water heater by my parents house. The prior water heater was venting into the furnace vent which vented into the chimney. Prior to that the water heater, it originally vented into the chimney by itself which was above where the furnace vented. My parents relocated the water heater about 20 years as they thought they would install a bathroom in the area where it originally was. They never installed a bathroom so I moved it back to that original location when I replaced it. After they relocated it, they filled in the vent hole with a brick and mortar.

My question is as follows... I am now venting in the original location and have removed the brick to expose the prior hole. There is a hole in the clay flue there as well.

Do I just fill in the empty spots with a partial brick and some mortar? Do I need to seal the crack between the brick and where the vent pipe goes through once I install the partial brick and mortar? E.g. Furnace cement, mortar, etc. Not sure how air tight this needs to be. I have attached a picture.

Thanks...

my code says you can not put an orphaned water heater into such a big flue. you must line it with a 4" liner. it will not heat the large chimney space enough to create a draft.
second problem is that you must have 12 inches of vertical pipe on the draft hood before you can turn 90 deg.

Thanks. I thought an "orphaned water heater" implied that there is no longer a furnace venting in the chimney as well? The furnace is still there too.

OK, then if it still shares the same flue liner, you are good to go.
just raise the first elbow up as close to 12 inches as you can. make sure to put 3 sheetmetal screws (equally spaced) in each joint and seal the chimney opening with any kind of cement product you have.