Image Processing in Bridge lost PSD originals HELP!

I am somewhat new to using Adobe Bridge CS4 super frequently, I have been processing batches of images mostly using the 'Image Process' function under tools>photoshop>image processing. I was using it to watermark my photos and size them down. It worked great, did everything I wanted it too and made it's own JPEG folder with all my processed images. HOWEVER I just discovered that when I process them it is somehow is taking the original image and flattening it so it looks like a JPEG even though the file still thinks it's a PSD file. The size is small and all the layers are gone, basically it looks EXACTLY like the JPEG file I'd just made but it's the original file and it's still a PSD (in theory!). I've been racking my brain trying to figure out when I'm doing wrong here! Been all over the internet trying to find a similar situation and I've had no luck. Any thoughts? I'd really appreciate the help. These particular photos are ready to go to print, but I've got my watermark on them and can't exactly remove the layer that isn't there anymore! HELP
Oona

Yes I was converting images from PSD to JPEG with the image processing but I was running an action (within the same dialog box) to make the file sizes much smaller for easy upload to the web? Does running an action affect the original as well as the processed images?

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