I realized that an uploaded document was not the correct version. I didn't need to correct any text in the post about the documenet, I just wanted to upload a new copy of the file and then correct the links in the post. So I uploaded the new file, corrected the links in the post, and then found an "orphan" post out there that was evidently created when I uploaded the second version of the file. I then deleted that orphan post and the new version of the file was also deleted. This does seem to be reproducible.
1. Use the built-in file uploader to upload a file. Check that the file is indeed uploaded (browse to the appropriate directory in wp-content or whatever). Navigate away from the "write post" screen.
2. Go to manage posts and search for a post using a term that was in the filename from step 1.
3. In my case, I find a post with an empty body and a title that comes from the name of the file that was uploaded. None of the "private," "draft," "published" buttons are checked.
4. Delete the post.
5. Go back and try to find the uploaded file. In my case, it's gone.
I have looked for other discussions of this problem, but haven't found them. For now my workaround is to upload the file some other way.
I do have the Organizer plugin installed, but generally find the built-in uploader sufficient and I'm mentioning that in case it might be part of the problem. http://imthi.com/organizer/