I'd removeall images that you are not sure about from the Trash, before you empty it. As you probaly know, ypu can simply do this by selecting them in the Trash and using the command "Put Back" fom the contextual pop-up menu, when you ctrl-click them. Before putting back, I'd flag the images, or assign a coöor-label, so you can recognize them easily, when they are back in there projects. Then you can compare them more thoroughly with their current versions, for example check, if they are sharing the same original image files. If you can find a common trait for all the trashed images, it will be easier to guess what caused them to be trashed.
I have no idea, what could move images to the trash, unless you accientally selected and deleted more images than you meant to. This can happen, when you reject images, so they are not displayed, or delete images from an album instead of removing them from an album. Also stacked images can contain more images than you are aware of, and you may be deleting a whole stack of images, when you only want to delete a single image.
That sounds like a good idea.
Yeah, I have no idea how those others got there. It's a fairly recent group of images (only taken last month), and I really have not had a chance to go through them. I must admit I very rarely toss anything in the trash via Aperture, so how these 900-odd versions got there is a bit of a mystery to me.