First, what is the model of your hard disk ? The backup boot
sector is located at a place unusual for a 512-sector disk.

Then, you have built the image after having started chkdsk twice,
nevertheless when I start chkdsk on the image, it still finds an
error. The error is about directory Django/GSWD/projects/old_microblog
which is just named microblog in the parent directory. This appears
to be a directory created on Windows as microblog, which you renamed
as old_microblog on Linux. I am surprised this was not fixed by
chkdsk on your computer.

The missing clusters found by chkdsk on your computer are related
to some earlier fixing of files created on Ubuntu. The first one
is about found.001/dir_00000000.chk which was obviously created
by Windows. The last three ones are related to git files such as
found.001/dir_00000000.chk/.git/objects/f9/cf35626bdb4bcbbb5....
but other files apparently created by the same process were not
flagged (such as found.001/dir_00000000.chk/microblog/settings.pyc)

It looks like Windows and Ubuntu do not read the same data.

Can you create on Windows a file a bit over 4096 bytes (for
example 5000 bytes), then switch to Ubuntu and *append* a few
bytes (for example "echo more data >> testfile"). Do not use
a text editor which would relocate the file after updating.
Check the time stamp of the file while on Ubuntu. Then switch
back to Windows. Is the file visible ? Has it been moved to a
quarantine directory (found.001) ? What is its time stamp, what
contents ?
(better use a partition different from the one for which you
sent the metadata, so that it remains meaningful).

> The notebook specs says that, and Gparted listing two disks
> of these sizes confirms that.

Can these specs be accessed on-line ?
I assume Gparted does not mention the SSD is used as a cache.

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https://bugs.launchpad.net/bugs/1280574

Title:
  Files modified on NTFS partition are seen as corrupted files in
  Windows

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