Ok this worked, I made a couple of mistake first but nothing bad. First it’s good to have a backup export, so I did a full backup in a zip file using document_exporter in the paperless shell of the old install (which I could still boot using the boot menu to roll back to the previous OS version temporarily).
This export.zip should be moved outside of the paperless storage, like a backup folder, just in case.
Then in the latest OS, fresh paperless-ngx install, I did mount an extra path from my hosted paperless folders to /usr/src/paperless/export (first I did mount on /export, but it was wrong).
Then I copied back the zip file there and run the document_importer but it failed. It asked for the manifest.json file, which is in the zip. So I unzipped (couldn’t do it directly in the paperless shell, was a mess), but in the end I should have not done that. Only the manifest.json (and maybe version.json) is needed as long as your document folder is still here with all document and mapped properly in the new instance.
Then I could run the importer, it gave me a couple error and warning due to the difference in the instance version but it looks like everything is back to normal. However some settings and the views might be missing. I figured out later that I just needed to restart paperless to reload all the restored settings and views.
I hope it might help other in the future.