I don't know why this happens to you, the only time I lose the scan in progress is when I accidentally target another planet while in system/global map.
Yup, I open the sys map all the time and the DSS continues scanning and finishes it, if you hoover again the object data will be displayed when scan is finished without needing to close/open the sys map again.
The only thing that makes the scan interrupt is selecting another object in sys map before the DSS has finished the scan. that action would untarget the object also from the cockpit and interrupt the DSS. But as long as you don't select another object, DSS goes on working.