by Usman Asar.
Nicolas, I have just sent you link(s) to video in pvt msg, else Howard will delete my post here
Your shadow copy purpose is shown half way through, but do watch full video as I have as well shown a crucial element while upgrading to a higher version (major upgrade).
Summarizing, the mistake you'd been doing was NOT creating separate database and moodle data folder for your individual sites. That I have as well addressed in that video.
Should anything comes up, feel free to ask, and feel free to distribute the link if someone else wants to understand Moodle Migration. As the site is limite to 2GB bandwidth, let me know if it exceeds and I will post the link somewhere else.