Is it possible to uncompress a PDF file?

I was told at work to compress thousands of old PDF files. When I first started I did them one at a time, then i was told to compress multiple at a time to do them faster, but for some reason maybe 100 of the PDF files reversed white and black. I was wondering if their was a program that I could uncompress a compressed PDF file or a program that I can run on the files to restore their images?