aperture hell! 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?