Hi,
I've never tried this in Autocal but it should be possible. I guess you need to run both extraction and postprocessing executables in a sequence, either directly or via a bat file e.g:
MSHE_Wbl_Ex.exe //apv My_WB_areas.WBL
MSHE_Wbl_Post.exe //apv My_WB_areas.WBL 1
MSHE_Wbl_Post.exe //apv My_WB_areas.WBL 1
MSHE_Wbl_Post.exe //apv My_WB_areas.WBL 2
In the above, the first command runs the Extraction phase of the water balance utility, while the subsequent commands run the Post-processing items in the water balance file. The number after the water balance file name indicates which Post-processing item to run. This is discussed in MIKE SHE User Guide, Section 3.5 (Using Batch Files) and more in-depth in Section 6.2 (Calculating Water Balances in Batch Mode).
Otherwise it is better to build up the autocal arguments step-by-step so that you ensure each argument is working as expected.
Hope this helps.
Elias