Are your raw files part of a raw+jpeg pair or raw-only?
When I tried to reproduce your problem, but for me the external edit is working as described in the manual.
- Set the "External Editor Format" to 16 bit psd in the "Export" preferences.
- Select the image in Aperture's browser and use the command "Photos > Edit with Adobe Photoshop CS 6"
- Edit Photoshop and use "File > Save", not "Save as".
What exactly do you see, when you are using Photoshop as an external editor?
As soon as I use "Photos > Edit with Adobe Photoshop CS 6", the new PSD version will appear alongside the raw, and after I save the file in Photoshop, the thumbnail will be updated.
Do you also see the new version appear, before Photoshop opens?
The only way I cannot see the versions side by side, is if I do not set the sorting in the browser to "Date", or if the search field is not cleared. You may want to check the sorting of the project and check for filters.
For example: Editing a raw-jpeg pair, first with "8bit tiff" export, then with "16bit psd" export.
If clearing filters and changing the sorting does not bring the original back, I'd try to repair the Aperture library - this may recover missing originals in a "Recovered" project.