Hi Alex,
If you can afford to rerun your simulation and don't mind using a bit more disk space, you could save scalar flowrate (Q) to your slf result file. Add it to your GRAPHIC PRINTOUT line.
example:
VARIABLES FOR GRAPHIC PRINTOUT : U,V,H,B.....Q;
After you open your results in BlueKenue, you simply have to run steps 7 through 9 (see Martin's answer), but this time Integrate on the Scalar Flowrate layer directly.
This has been a time saver for me on several occasions. I've noticed a very slight difference between discharge calculated this way and what you get if you run steps 1-9 but that's probably due to discretization differences. In my case that difference is generally less than 0.5 %.
Regards,
jeremie