Thanks for all for inputs, these are some of my doubts after going through manuals,
The "Refuel" switch position input is directly connected to the FQI Computer,
the FQI computer supposed to close intercell transfer valves at beginning of refueling (if they are open in flight that just concluded).
Intercell transfer valves control logic is probably controlled by software inside FQI,
when refuel switch is returned to "off" it may be enabling the control logic to open in flight when low quantity sensed in inner cell. So if you do not return the switch to "off",it may affect this operation.
Any time new fuel is added to tanks,the FQI calculates new density and capacitive index for accurate fuel quantity indication,if the switch is left in "Refuel" it may affect this calculation inside computer.
Now a days many functions are done by software inside the computer based on certain algorithms and hardware inputs, so it is difficult to come to any valid conclusion unless it is given in the manual.