As reported by Edwin here:
I just noticed this lately when our user reported that some Internal Use Inventory documents are missing after complete. Upon tracing we found out that, the user has set internal use qty for all lines to 0. When completed, the document are processed as Physical Inventory document and worse the qty book is 0.
So basically this will clear up the storage.
This behaviour is observed at Adempiere361 and I've just confirmed that this is still a current issue on demo.idempiere.com.
A quick solution is to add a flag isInternalUse on M_Inventory to differ the document processing.
Why do you think?