When you delete photos in Aperture they get moved to the Trash container (the last item in the Recent section in the leftmost column of the Aperture window). They *should* remain there until you select Empty Aperture Trash from the Aperture menu, at which point they are removed from the Aperture library and put into the System Trash. Have you looked in both places?
To remove filters, as Frank suggested, clear the search fields in the Browser:
Each library item may have its own filter set, so select the the project with missing images, to check for filters, and the containg folders as well. If the search fields do not show "Showing all" or All items", reset them.
Thanks to you and Frank for pointing out the filters. I undid them and retrieved some photos, but still can't find the ones I am looking for. I must somehow have deleted them. And then maybe I emptied my trash after I deleted them - I don't recall this, but it's the only thing I can imagine. I cannot find any photos whatsoever from the dates I am looking for - even when I undo the filters for those dates.
Any suggestions for the best software to search and undelete deleted files on the mac? I tried Disk Rescue demo version but it did not locate any .NEF files, which these were.
I undid them and retrieved some photos, but still can't find the ones I am looking for.
Did Aperture crash recently, or did you force quit it? Then your Aperture library may need repairing. If you have not done so already, I'd recommend to use the Aperture First Aid Tools to repair the permissions and Aperture dabase, see: Repairing and Rebuilding Your Aperture Library: Aperture 3 User Manual
The first two options - repairing permissions and repairing the database - should not take too long, but the third - rebuilding - may take a long time for a large library. You should make sure your backup is current, before rebuilding.
Is your library referenced or managed? If you store your original image files in the Aperture library on import and not reference them outside, you could search for them directly inside the Aperture library package: ctrl-click the library package, select "Show Package Contents" and then open the "Masters" folder inside. This folder stores your raw files in subfolders arranged by the date of the import session. Do you see your missing images there?
Any suggestions for the best software to search and undelete deleted files on the mac?
You might have a look at http://www.mediarecoverysoftware.com
I never used that program, but it promises to handle Nikon raw files.
You may have the rare case of an invisible filter. Frank could much better explain this to you, for it was him who worked out the solution for this, see: