In your present position you will need to find a program that will identify each individual file on your CD/DVD on a file by file basis, it will then have to establish what type of file it is and what year it belongs to and then copy it back to your new HDD into the right place. I'm sorry to say I have not heard of one that can do this yet.
It's not impossible and should be fairly stright forward it's just that I think you will need a bespoke program to do it. Do you know any programmers.
However for the future I would recommend Nero Burning Rom to save your files from the external HDD to the CD/DVD's this would meet all your requirments ie. Full Disks and it would also maintain the intergrity of your file structures plus it would allow you to reload an individual file.
I'm sure someone else on the forum may have other and better suggestions.