Using Illustrator CC, we save all our CMYK illustration files in PDF format. I just encountered a file where the copied half of the file (the design just copied over to the second half of the paper) printed with darker colors. I tried copy/pasting the correct half to a new file and duplicating the design, thinking maybe the file was damaged somehow, but that newly copied second half in that file also became darker upon printing.
I also tried duplicating the layers to copy the design with the same ending. I exported the file as a tiff and no such discoloration happens, so it's not in my layer settings. To work around for now, I've exported the design as a tiff and reimported & resaved it as a pdf. That appears to have it printing as expected, but is not a great permanent solution as the tiff is not editable.
Should I need to make changes in the future, I'll have to go back to the original PDF file, edit, export, import & resave all over again. I'd appreciate any insight as it's super bizarre.