All the apps from the Color have come onto the HD but none of the files...such as the EZPDF viewer files.
Is there any way to get them on my HD?
You need to get your personal files onto the HD the same way you got them on your Nook Color. You can copy them from your computer to the HD using the USB cable or re-download them from the internet. I personally always keep copies of my PDF files on my computer for backup.