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I did the exact same thing 3 or so years ago. Thankfully I already had a backup but it was a bit nerve wracking to log in to next cloud and it was empty and then browsing the mount and having it also be empty
there's user error in this case, but imho it's a bug that the initialization scripts deletes hundreds of gb without any warning or an override command. Files weren't even owned by www-data! Ok to copy new install files, but not wipe clean...
if one day some web exploit manages to delete/rename/move the file that the script detects as "installation done", it could lead to a worldwide massive data loss when the server reboots