The size of the flue has to be appropriate for the heat load of the device. If it's too big around or too tall the flu gas will cool and stop rising before it reaches the top. then the rest will vent out all over your basement or whatever.
but if it's sized properly there is nothing wrong with having a single water heater on a single flue.
This is standard stuff for the repair/install guys though, I'm surprised that they took off the other device without making sure that it was OK for the water heater. I'd call the guys back that installed the furnace and get them to come out and tell you if your current flue is OK for just the water heater.
If it's too big around then it's easy enough for them to add a liner to reduce the internal diameter to accommodate the water heater. But this should have been part of the estimate/process of putting in the new furnace.
If they can tell you from their records what the flue size was and what was required by your water heater and that it's OK, then thats probably OK. If they just want to assure you without actually having any information for real I'd be worried. But then, if they are that much of a hack I'd be worried about the new furnace install as well! If thats the case then get ahold of a home inspector who specializes in checking this stuff out. It will cost you to have him out, but you'll know for sure that it's OK, or you'll know for sure that you need to do something.
