I'm stumped. The building was built in 1893 so things often don't make much sense. When emptying the old hot water heater (turned off cold water supply, opened hot water faucet) I had trouble draining the tank. For some reason it created a vacuum and there was cold water entering the tank from the hot water outlet on the tank. So basically after awhile of trying to drain the tank and not getting anywhere I figured out that there was a shut off valve for the hot water line waaaaay up in the boiler room. So basically I isolated the hot water heater and used a pump to drain the tank.
First question, where the heck was all the cold water coming from? As far As I know the hot water line coming from the hot water heater just goes to the sinks and tub in the house? I don't understand why the tank would keep filling up from that line.
Second question, after hooking up the new hot water heater, the sink down stairs runs very hot water but the upstairs only runs lukewarm water for awhile then runs colder water. Am I missing something?

What you're missing is a cross connection between hot and cold. This could be caused by one of two things,
1) A mistake in the design of the water system. Any plumbing work done lately besides replacing the heater? **OR**
2) This could be crossed in a One handled mixing valve allowing cold water to enter the hot water side.

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there was cold water entering the tank from the hot water outlet on the tank. I used a pump to drain the tank.

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This is not right! You will have to track the cold water back to then source. I would start by shutting off EVERY one handled faucets at the angle stops. This includes the tub and shower valves. Now do what you did to get cold water in the hot water feed to the heater, If no cold water comes then open up the angle stops one fixture at a time while checking the heater feed for cold water. Let me know what you find. good luck, Tom

Yes, we just renovated the second floor of the building. NY state code required all plumbing and electric to be done my a licensed tech. So, all the plumbing was switched to pex.I inspected everything as I was doing all the framing. Its all very straight forward. Both the bathroom and kitchen sinks use one handle valves. I will shut them off and see if the tub puts out hot water. The shower isn't finished yet so I can't try that out, it has two valves anyway.
Can you explain to me why everything would work fine with the old hot water heater and only now with a new heater, start to screw up?
If it is the one handled faucet, Is there just a gasket in there that popped which would allow cold water through the hot water line?

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Can you explain to me why everything would work fine with the old hot water heater and only now with a new heater, start to screw up?

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But you changed more then just the heater didn't you? Just because you had a licensed plumber to the work doesn't mean he couldn't make a mistake. Also in replacing the heater some minerals might have been dislodged and got into a faucet cartridge causing the problem.

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If it is the one handled faucet, Is there just a gasket in there that popped which would allow cold water through the hot water line?

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If a faucet is the culprit replacing the cartridge and flushing the valve should solve the problem. Good luck, Tom

I shut off both sinks and still have lukewarm water coming out of the tub. The plumbers only added new lines from the copper that ran to upstairs. Also, we have been here a month already with no problems. It only started after drainig the water heater. I guess I need to some how expose the pipe that runs upstairs to see if it was taped into anywhere?

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I shut off both sinks and still have lukewarm water coming out of the tub.

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not the way I told you to check.
One more time.

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You will have to track the cold water back to then source. I would start by shutting off EVERY one handled faucets at the angle stops. This includes Tub and shower, kitchen sink and every one handled valve, This includes the tub and shower valves. Now do what you did to get cold water in the hot water feed to the heater,

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ere was cold water entering the tank from the hot water outlet on the tank.

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If no cold water comes then open up the angle stops one fixture at a time while checking the heater feed for cold water. Let me know what you find.

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this won't be easy. You will have to sutd down every one handled faucet in the place, If it's a faucet your heater will be working normally, If there's still a problem I would check the new piping. Good luck, Tom