Hi,
What kind of substitution do you use? A standard one of OBBH? In this case, I believe, you changed the settings for BSEG-KBLNR field to be eligible for substitution. In certain cases, this might work, but for some fields it won't, which seems to be the case here. So, if you substitute EMF (I guess, via user-exit) for these postings, do the same also for WBS: since, you know how to derive EMF, you should be able to do the same for WBS, as according to you, they are linked.
Regards,
Eli