Yeah, the workaround I've used when having check-in problems. Re-checkout your data. With the checkout data, start an ArcMap Edit session, delete all records, then use the object loader to load your edited data into the checkout data. Checkin the data, it will see it as all deletes and adds so you really can't see the changes, if you have multiple editing users this is not what you want to do. In our case we had multiple users but they were assigned a specific area so we could just drop/add that area...