Summary: When editing a previously uploaded file by uploading a new version, clicking on "Save" instead of "Check in" will save the new file's metadata, but not its content.

Relevant (as far as I can tell) configuration details:

Version: 4.1 Build: 4.1.3541

Global settings, category "Files"
Store files in file system: True
Store files in database: True
Generate thumbnails: True
Redirect files to disk: True
Check if files are published: True
Check files permissions: True

Global settings, category "Content management"
Use automatic version numbering: True
Use check in/check out: True
Version history length: 20

Steps to reproduce:

1. Create a new document of type "File".
2. Upload a small image file.
3. Save the document.
4. Check the document in.
5. Publish the document.
6. Verify that the image is available on the live site at the desired URL.
7. Check the document out.
8. On the "Form" tab, click on the "Update" icon to upload a different file.
9. Select a different image and accept the choice.
10. Hover over the new file name to verify that the new image has been uploaded.
11. Save the document (click on "Save" under the "Form" tab).
12. Hover over the file name. For me, at least, it has now reverted to the original image.
13. Check the Preview. It's the original image.
14. Check in and Publish the document.
15. Verify that the image at the public URL is the original, not the new image.

Expected outcome: the document is updated to contain the second image.

Actual outcome: the document's metadata (file name, file size, dimensions) reflect the second image, but the binary data is that of the first.

If, in step 11, you check the document in rather than saving it, the outcome is as expected, with the second image replacing the first. It's just if you click "Save" at this point that it goes off the rails. It appears to be reproducible with files of other types, not just images. I haven't reproduced it with other document types, just CMS.File.