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I'm running a closed loop cooling system with a pump, with a final product condenser and a dephlegmator at the top of the column.

I will daisy chain from product condenser output to deplegmator input. So far so good. But to add control to the deplegmator water, I will put a needle valve on the input, with a tee so that some of the product condenser output can return to the tank, while some the rest can go to the dephlegmator input. Makes sense. However, the output from the dephlegmator will need to go somewhere, and by somewhere, I mean back to the tank, which means it will need to join into the return line.

What I'm worried about is backflow. I want to make sure the combined drain won't run back up the wrong way from the dephlegmator, or run back up to the dephlegmator input.

I'm not sure I can use check valves because of the potential pressure difference due to different flowrates.

Anyone done anything similar?

I think you will be OK .

If it were me, I would make both have their own cold supply and not chain them together. I like to tie the outputs together after the controller valve. But you know whatever floats your tuna boat.

Edit. Just looked again at your diagram. It's early.

I see no real problems.
There is a pressure from the water supply, so the flow in the productcondenser will be from end to begin. I can not imagine large backflow from output of product condenser to output of dephlegmator, for the resistance over the dephlegmator is greater than over de output hose of the product condenser. You can prevent the risk of backflow even more, if you let the outlet pipe(s) spill into open air, a bit over the water level in your supply tank.

Another point may be that you need more water in the dephlegmator than in the condenser, but that makes your product only a bit cooler than before and there is no harm in that.