When I took delivery of my Kubota M8540, I noticed a u-shaped hydraulic line in the toolbox. I asked what this was and the mechanic said it came off of the tractor when the FEL was installed.
It is basically a return line from the supply (pressure) side to the return side. When no valves are installed, it completes the loop. When you install a FEL, this is where you tap into the system.
There is a BIG sticker down near my FEL hydraulic valve (not joystick, but valve) that states you must re-install the u-shaped line if the FEL valve is removed... and NOT simply cap the lines. This makes perfect sense.
Anyway, unplugging the the QD couplers to remove the FEL does not remove the FEL valve. (On my Kubota anyway. I imagine on most Kubotas and on most other brands that have QDs.) The joystick in neutral allows the FEL valve to let fluid flow and return. This is the same whether the FEL is installed or not.
Now, if you tap into the system and remove the FEL valve, you have to provide the return yourself. In my case, I have the original line handy.
The main reason I know this is because I recently installed a 3rd function valve myself. To do this, you have to tap into the hydraulic system and re-route the pass-thru. (This is in addition to other things of course.) Instead of the return from the FEL valve going back to the main return, it goes into the supply of the 3rd function valve. Then the return from the 3rd function valve goes back to the main return. (Or vice-versa, I don't remeber. The 3rd function valve may be first, but the point is valid though.)
When all valves in the system are in neutral, fluid freely flows throughout the entire system. Nothing is blocked. When one valve in the system is opened, fluid is routed to the implement (cylinder, pump, etc.). When the system GPM exceeds the implement the bypass is used.