I've had a good Google but not found anything definitive, so I'll ask for some general comments here. :-)
SS has long had an issue with Files & Images when there are a large number of files. Any server has a finite amount of resources, but users can add an unlimited number of files; so given enough files to process, regardless of how much RAM and execution time you throw at the problem, operations on folders can die midway, leaving the File table out of sync.
Are there any plans to move operations like these to offline processes?