Any constructive advice, help, appreciated.

BACKGROUND:
Drive is Running SMART and no notice of any issues.

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 two 500 GS drives have had little use and are backup drives ONLY.

The problem logical extended drive partition contains MANY small files.

I have been gradually noticing some weird things with the file system. For example when
creating a new folder (directory), I'll type one or two characters and then the cursor will jump to a
different folder. Or I'll look for a folder and it seems out of place.

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."

WHAT I"VE DONE TO DATE
Noted the file names of several files in the chkdsk "found" directory on the "son".
I then went to the "grandfather" (son offline) to see if I could find the same files and open them.
I was able to locate these files, and find them in the correct directory and also open and view them.

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 the same 53 "found" file file folders
containing files.

Ran WD's "Lifeguard Tools for Windows" on the "son" and says "son" OK.

I then ran TestDisk on the "son" and says everything OK. So assume chkdsk corrected any issues.
Plan to again clone the "grandfather" to "father" and run TestDisk to see if any file system errors noted.

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 DiskId are the same on each drive.
Windows 7 (diskmgt.msc) doesn't like this and while I can bring both drives on-line (one bootable) with
"diskmgt.msc", I wonder if having two DiskId's the same when starting the compuer may be causing issues. Should I Change the DiskId offline before I try to bring the drive on-line?
--------------------------------------------------------------
3) I'm a little confused
--------------------------------------------------------------
Why can I locate and see the files on the "grandfather" when a cloning of this partition and
re-running chkdsk finds errors?

4) With Clonzilla, do I need to unmount the drives before I "poweroff"?

5) If I do a file by file copy (using XCOPY, or ddrescue. TESTDisk, or some other preferred software ???)
from the "grandfather" to a new partition, will this keep the files in the correct directory and
HOPEFULLY have the files be correct?

6) Is having a large number of small files possibly causing my issue?
Note that under each folder there is a small number of files, but taken together on the
entire partition there are 32 GB of small sized files?

Can you show us your CHKDSK log file?

https://www.sevenforums.com/general-discussion/96932-location-chkdsk-log-file-after-scan.html

Can you check the state of the NTFS "dirty bit" for your grandfather?

fsutil dirty query X:

X: is the drive letter.

_________________
A backup a day keeps DR away.

"...Is it possible to clone or copy partition to partition from a larger drive (500 GB) to a smaller drive (250 GB)?" I don't think cloning will work for partition to partition; however, I do know a full image of the source partition can be "squeezed" onto a smaller target partition
-- if something similar to Macrium Reflect's Intelligent Copy is used
(meaning only occupied clusters/sectors are shoved into the full image)
-- if the source partition's data is less byte-space than the target partition

_________________
"Take care of thy backups and thy restores shall take care of thee." Ben Franklin revisited

If "Intelligent Copy" is anything like Acronis True Image, it will first test the integrity/consistency of the source file system. If the test fails, as it undoubtedly will in the "grandfather's" case, the copy does not go ahead.

_________________
A backup a day keeps DR away.