Jacob,
Assuming that it is an inbound IDOC. Venu's comment is that in WE02/5, the billing document no. can be seen. If this is true, then this billing document no. should also be updated in VBRK.
If this is not the case, now going in to more nuances...then there is a flaw in the design. So if inbound idoc has a billing document number which can be seen in idoc display mode WE05, then it must be also created in ECC. If due to some reason, IDOC can not create a bill no. in ECC, then WE05 should not have a billing doc no.
TW