Rob,
Having looked at the code, I’m fairly confident that there is no indexing. It is parsing the directories on the fly. I encountered a similar issue, wherein directories that I was deleting were reappearing. It turned out that the problem was that my page included fileup shortcodes for those directories, where the makedir parameter was true.
Yeah, what @travisr said. No indexing. If individual files are being displayed in a file away table, then those files have not been deleted. There is no way a file would show up if it doesn’t exist.
Unless the page is being cached. I clear my website cache when I update files.
Ah, yeah. Good point. I would think it would be a good idea to set dynamic pages like file away pages not to be cached in the first place, unless there’s a ton of non-dynamic content. But even then…