We built some DLLs to generate "subsets" of our documents for certain postprocessing applications outside of the FM GUI. These subsets are sometimes not as complete as the EDD/XSD requires. So the pop-up is legal - but keeps us from doing the postprocessing in an over-night batch job.
Another point where the same pop-up is a major PITA is when a complex operation - automated as DLL - needs to write an "almost perfect" (temporary) document to disk.
I tried all (documented) properties of the F_ApiSave method, but nothing affected this "WARNING".