Master files consolidated into Aperture library and now lost...

Aperture 3.1 appears to be doing strange things with a few of my master RAW files stored in the Aperture Library. I consolidated several files (as a copy) into the library and the files showed that they were non-referenced for several months but now I get the yellow triangle and "Referenced File" arrow on the file metadata.
Any ideas Aperture folks?

I havent found an easier way. It happened to me once, and i just deleted all of the songs out of iTunes, but not out of my hard drive. then i replaced them all in the library. It took like 12 hours cuz i have 15 GB worth, but at least i didnt have any more doubles

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