My Baseboard water circulation heater system has 3 Zones.
The 3rd zone on my third floor is not working. The circulation water pipes near the heating unit become hot when I turn on the thrmostat and then cools down. I have no heat on the 3rd floor, but at time the unit works.

Check for
Air in line if so bleed 3rd floor area.
Check for water pressure in boiler if low increase.
Make sure zone valve or 3rd floor pump is working.

I would think you have a T-stat on your top floor where you have no heat, and it is connected to a zone valve or control panel that either starts another pump, or opens a zone valve. Go to the boiler and look for the zone valve that goes to your upstairs zone... (they will look like little boxes on your hot water supply pipiing) if it is a current Honeywell type, you will find a small lever to move to the open position, and put the level in the little notch to hold it open... to give you heat to that Zone. ( this is only a tempory fix, being that every time other zones call for heat and the pump starts, this zone will heat all the time... An easy way to find that one, it to turn up the other T-stats and the zone valve that is not open ( look at the manual level, and move it to the open position, if you feel NO resistance on the lever, it is open, and that is NOT the valve) You will have to call a contractor to change them, being that on some you have to either drain down the boiler, and cut out the bad valve and solder in a new one, and on the newer valves, you just change the motor head part. You also can look for loose wires that may have come off the valve, they are powered by 24 volts.