Aperture sees no CR2, but Finder does

It's driving me mad. The CR2-raws are in the correct folder, with finder i can see and open them (preview). Aperture shows them in the browser, but the line 'show in finder' is gone. When asked for 'Manage referenced files', Aperture tells me: 'No referenced file. The selection doesn't use any referenced files.'
But, they are there. It's just Aperture that fails to see them.
I can relocate the master. And I can export to an new master and rename. Than I can import and start of over again.
It's a lot of professional pictures for clients. I really can't afford to redo all the import and enhancing.
Anybody heard of this problem?
I pray there is a solution.
Bart

Thank you DLS, for your swift answer.
All files were imported to store in their 'current location'.
I've been working on this assignment for 3 months. All of the first shots are now - apperently - managed. Some of them are gone. Shots of last weeks however are referenced. Very strange and very unwanted.
It feels as if all my images are gone, allthoug they're really not. Even iPhoto can see them.
It does annoy me that Aperture tries to think for me and manages my files and makes others invisible.
And it makes me feel stupid. Perhaps I am?
Looking at the numerous post on the subject of the Aperture database, it appears to me that I'm not the only one and Apple has not done a good job.
I assume that now I have my images stored in the Aperture library. I can export them to useable versions for my client. And I will export all masters to a seperate disk.
Again, thanks for your suggestion.
Greetings from an extemely cold Netherlands (-14 degr celcius here is very rare)
Bart

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