Aperture overwrites files with same name

My canon camera was setup with filename numbering to 0001. When the camera reached the 9999, it restarted the numbering to 0001. I didn't noticed the file names since I just import my picture with aperture.

Now after some time I figured out that the old files, like first 0001.jpg version is no more available and 0001 is always the last one picture imported.

It looks like I lost a lot of pictures! Is weird!

There is anyway to get back all pictures out of aperture?