I have a standard cost customer who is using the 'On-hand aggregation by financial dimension’ job to tidy up On-hand records with zero quantity (but some open financial amount). They also started using the 'Warehouse management on-hand entries cleanup' to help with performance of On-hand inquiries. I did not hear that the latter reversed the benefits they were getting from the former. Perhaps it was the Consistency checker; I would not expect that you should need to run the consistency checker as part of routine maintenance.
Regarding KB2951209, check if you are able to change the cost of one of your standard costed items.