non-comaptible image format after el capitan update

Sean, could you explain a bit more?

and as soon as I did, most of my Apeture library was lost (about 10 years of work).

In what way was your Aperture library lost? Wa it not possible to update Aperture to version 3.6, so it would run on El Capitan? Or could Aperture not open the library?

I realized that I had backed-up all of my images not as originals but as apeture files.

Do you mean, your backup are Aperture libraries or vaults? Which version of Aperture?

Not a big deal untill I uploaded everything and 90% of the images were blank with a "non compatible image format" message.

Where did you upload the Aperture "files" to? which phot application are you using on El Capitan?

Since only the RAW images are showing the "unsupported RAW format" warning, have you tried to reprocess the RAW files? WIth "Photos > Reprocess Original"?

If that is not possible, try to reinstall the RAW support. I don't know which camera created the files, but look at Apple's Support Downloads page.

What is the RAW format of your image files?

Try, if Aperture can still read the RAW format by copying one of the files out of the library and reimporting it. File > Export > Original should work, even if the format is not supported.

Then try to import it again. Is the file now supported? If Aperture does not recognize the format, test, if the Photos.app can read it. It uses the same RAW support. This will tell you, if the problem is Aperture specific or system specific.

So Aperture sees the originals as missing? Look inside the Aperture library to check, if the originals really are missing.

Ctrl-click the library, select Show Package contents, open the Masters folder. If the originals are there, copy one of the RAW files out of the package. Then reimport it.

Have you ctrl-clicked (or right-clicked) the Aperture Library in the Finder?

The contextual menu pooping up should be looking like this:

And "Show Package Contents" should be showing you all folders inside your Aperture library.

If the Library has been opened by Aperture 3.6, it should look like this:

If there is no Masters folder in an Aperture 3.6 library, Aperture is referencing the original image files outside the Aperture library. Then you need to restore the folders with the referenced original files as well.

To test if your original files are referenced and have not been imported into the library create a smart album:

File > New > Smart album.

Click "Add Rule" and add the rule "File Status is referenced".

Make a second smart album wth the rule: "File Status is missing".

Are your files referenced and missing?

Once you have confirmed the originals are inside your package, I suggest doing a Repair/Rebuild to see if this re-links the images in Aperture. Hold down Option+Command keys on launch.