> I haven't touched ntfs-3g, only copied/installed the plugin

Good to know this is usable, though it was not part of the design. You
probably cannot browse the OneDrive directory, but apparently you can
access files (and browse subdirectories) when you know their path.
Despite the inconvenience this should be safe.

In the test scenario, I wanted to see why LibreOffice defeats the
synchronization, which I expected to be apparent by comparing the
ntfsinfo before and after an update of a synchronized file by
LibreOffice (with no further interference from Windows). Your second and
your third ntfsinfo are about different files, so I cannot tell.

Expected scenario :
1) Create a file on Windows and get it synchronized.
2) Reboot to Ubuntu
3) Extract the ntfsinfo
4) Update the file using LibreOffice (and save it without creating a new file)
5) Extract again the ntfsinfo
6) (Optionally) Reboot to Windows, and check the file cannot be synchronized 
any more.

In your second ntfsinfo, I see that an object id has been added
(probably to reference the cloud copy). I suspect it was removed by
LibreOffice, and if its scenario for saving the updated file is to
create a new file and then to rename it like the initial one, then the
object id is lost and Windows cannot associate it with the cloud copy
any more.

If LibreOffice removes the object id, I see no solution.

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https://bugs.launchpad.net/bugs/1728354

Title:
  ntfs: unsupported reparse point

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