MPEG Streamclip Altered Original files.

I recently did a video shoot with a Canon 7D. I loaded 2 16gb cards onto a Lacie Rugged drive into seperate folders. After the shoot all the original files worked fine for playback with Quicktime and editing.

I then used MPEG Streamclip to convert the first cards footage to Apple ProRes. The harddrive ran out of memory halfway through the conversion and MPEG Streamclip canceled the batch conversion.

I went back to the original files and only about 5 random few out of 90 shots would still work with quicktime and editing while the rest no longer open. I read somewhere that if you don't rename the newly converted files then something happens so I deleted the new ProRes files. Nothing changed. I'm guessing that MPEG Streamclip altered the original files somehow?

When trying to open in Quicktime Player 7 I get "The movie could not be opened. The end of the file was reached."

I then tried to open the now working files in VLC and they work fine.

All the footage from the second card all works fine still.

I used VideoSpec to look at what was going on and compare between a working clip and a not working one. There were no difference in format or anything other than duration.

Container: MOV - Quicktime

Format: H.264/MPEG-4 AVC

Encoding Profile: Baseline@L5.0

Please help me get these files working again! I can not recreate this footage!!!! I know the information is still all there because the files can be played with VLC, I just can't edit with them anymore...