Aperture Duplicates

Are you using any tools, that automatically import to Aperture?

An Autoimport Folder, or My Photo Stream?

Have you been using plug-ins or external editors, that are saving photos back to the Aperture Library?

I have occasionally seen a duplicate folder in Masters, when I used an external Editor, that wrote directly to the Masters folder.

To fix this, I would select all items in Aperture and export a new Library.

Do you have an external drive with enough free storage, so you can recreate your library by exporting?

Select everything - projects and albums at once, then use the command "File > export > Export items as a new Library".

Exporting a library should omit the redundant items in the Masters folder.

I would not use a duplicate cleaner, that modifies the Library directly. It could damage the library beyond repair.

Last night, I did start exporting parts as new libraries, and found that the new libraries had all the expected files but were 1/2, 1/3, 1/4 the size of the libraries that I started with

That is good. At least it will allow you to create a backup without the duplicates.

Where is your Aperture Library stored? Is it on your system volume or on an external volume?

"external RAID", that should be unproblematic, as long as the file system format is MacOS Extended (Journaled), and the drive is locally mounted.