Yes, I have had this problem. It was less severe in my case, in that the duplicates appeared to be dupes of the thumbnail, so they were easy to tell from the original.

There are a couple things you can do to recover the photos. First, in Aperture, they may still be in Aperture's trash can "folder". Everything you deleted should be in there if you haven't manually emptied it. You'll still need to figure out which one is the original and manually move it out of the trash.

The other thing you can do is go into the Finder and locate the Aperture library. (It's usually in your home directory under "Pictures" and is named "Aperture Library.aplibrary" unless you named it something else.) Once you've found it, you can control-click (or right-click) on it and choose "Show Package Contents". In there you'll see a folder named "Masters". This contains the master files for all of your images. If you shoot RAW, your RAW files will be somewhere in this folder. (It's a hierarchy arranged by year, then by month, then by day.)

I don't know if it's possible to recover edited versions of your photos without running Aperture, since it generally just saves a link to the master, and the recipe for how to adjust the image rather than actually saving the pixels of the edited image. It recreates the image from the master and adjustments every time you bring it up in the app.