Dear Saurabh,
if you stop you simulation in Flair with the Stop Cycle / Stop Run buttons or you are using the fluka.stop / rfluka.stop files (See for Feature to pause simulation execution - #4 by horvathd more details), then FLUKA will generate the requested output files as it would normally by reaching the last primary.
If you kill the actual CPU process, then no output file is created and the current state of the simlation is lost.
Cheers,
David