Dear Jose and Barbara,
Integrating scalar flow following that procedure won't take into account the direction of the flow regarding the cross section orientation, leading to unexpected results in a fair chunk of cases.
Just to name a trivial one, drawing a parallel line to the flow direction in a river/channel and integrating directly scalar flow "Q" results in a discharge really different to 0 (or something really really close to it).
The appropriate methodology using bluekenue would be to print I and J (components of the scalar flow field) and integrate along a line,
as mentioned in this discussion.
On the other hand, I believe PostTelemac (Artelia's plugin for QGis) has a tool to calculate discharge over time in a defined section, really useful if you are dealing with a unsteady state model.
Regards,
José Díaz.