Data Recovery - Steps to Take

Any constructive advice, help, appreciated.

BACKGROUND:
I use Clonzilla for cloning.

I have my Primary Disk (son - 250 GB), a day old clone (father - 500 GB), and a week old clone (grandfather - 500 GB).

The problem drive partition contains MANY small files.

I ran chkdsk on the "son" and supposedly files were recovered but were put in 53 chkdsk "found" directories with each chkdsk directory containing numerous folders and files.

I decided to see what results I would get using chkdsk on the "father". It was the same as the 'son".
Boat load of folders and files in 53 chkdsk directories.

I have NOT touched the "grandfather."

PROBLEM:
Because there are so many files and folders, it will be a BIG task to try and figure out where they go
on either the "son" or the "father".

QUESTIONS HOPING SOMEONE CAN ANSWER:
1) Is it possible to clone or copy partition to partition from a larger drive (500 GB) to a smaller drive (250 GB)?
2) Since I'm cloning drives, the Volume Serial Numbers are the same on each drive.
Windows 7 (diskmgt.msc) doesn't like this and while I can bring both drives (one bootable) with
"diskmgt.msc", I wonder if having two volume serial numbers the same when starting the compuer may be causing issues?
3) If I write a program to change the volume serial number after cloning, will this cause any problems either with the OS or the Hard Disk by doing this -- some hidden things unknown to me -- when I try and bring both drives on-line?

HOW I THOUGHT I WOULD PROCEED -- FEEDBACK / SUGGESTIONS PLEASE
1) Copy the "grandfather" to the "father", and then run chkdsk again to see if the "new father" has any issues.
2) If "new father" is OK, then exact about 10 files I need from the "son" to the "new father" and say I'm good to go. Then clone "new father" to the "son".
3) If "new father" has same problems as the "son" and "original father" -- ie. 53 chkdsk directories,
then use the "grandfather" to identify and locate the correct file and folder locations for these chkdsk folders and files, and then move them from the chkdsk found folder to where they belong on the "new father".

By the sounds of it all backups are damaged so can't be used. The question is the drive faulty go-to disk makers site they normally have test software to check their drive, chkdsk is a generic test looking mostly at file system structure but makers will look at the disk it's self

Sometimes, I will also need to recover my data if my computer has problems, maybe someone can provide more situations about losing data. Thanks a lot:)

Thanks for responses to date.
Whether the drive "son" is bad is ???, as never had an issue or notification of any sort.
Running SMART, but don't believe this monitors the NFTS file system.
What I've done so far, is note the file names of several files in the chkdsk "found" directory on the "son".
I then went to the "grandfather" to see if I could find the same files and open them.
I was able to locate these files, and view them on the "grandfather".
I then cloned FROM the "grandfather" (have Not run chkdsk on grandfather) TO the "father".
After cloning, I again ran chkdsk on the "father" and received file errors.
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SO, I'm a little confused
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Why can I locate and see the files on the "grandfather" when a copy of these files says they have errors?

What I would like to do next is clean and reset (0) the data partition on the "father"
-- any help with identifying a cmd line function to do this appreciated -----
Then plan to use XCOPY to copy the same partition on the "grandfather" to the "father"
Then run chkdsk again and see what I get.
I hoping copying the files rather than cloning them may eliminate the noted errors.