Hi.
Just had the same problem as you had. Like you I cannot find any documentation. But in the same bin folder there is a document entitled MShe_FlowThroughLine.pfs.
I followed the syntax provided there and tried it out for my own little case. Worked fine.
The grid code dfs2-file with the line which you want to calculate flow through, should be neighbouring cells of 1 and 2, where your line is the 1's and the 2's indicates the direction which the programme should calculate the flow through. I.e. it will calculate the flow from your 1's to your 2's. (Found that out 'cuz I first tried to make my lines just of 1's, and then got the error message "ERROR : No pairs of neighbour cells with code 1 and 2 found inside the model area.").
In my case the 1-cells were located on some of the boundary cells (and the 2's of course within the model area), so that works fine, the 1's do not need to be *within* the model area.