The behavior you're describing — /home/benjamin_loison/ (and folders inside it) only existing while that user is logged in, and not being visible as root otherwise — is the classic symptom of an encrypted home directory (eCryptfs), which Linux Mint offered during installation. The files aren't missing; the home directory is only mounted/decrypted when the user authenticates.

Check

As root (or from another account), look at:

ls -la /home/
ls -la /home/.ecryptfs/
getent passwd benjamin_loison

• If you see /home/.ecryptfs/benjamin_loison and /home/benjamin_loison is an empty mountpoint (or contains just .ecryptfs/.Private symlinks), the home is encrypted.

Access without a graphical login

Option 1 — text console login (easiest): Switch to a TTY (Ctrl+Alt+F3), log in as benjamin_loison. That mounts and decrypts the home directory. You can then work there, or from a root shell while the session is active.

Option 2 — recover the data as root (no user login at all):

sudo apt install ecryptfs-utils
sudo ecryptfs-recover-private /home/.ecryptfs/benjamin_loison

It asks for the user's login password (or the mount passphrase, stored in /home/.ecryptfs/benjamin_loison/.ecryptfs/wrapped-passphrase, unwrapped via ecryptfs-unwrap-passphrase). The data is then mounted read-only (add -r is default; use ecryptfs-recover-private --rw ... for read-write) under a temporary mount, typically /tmp/ecryptfs.XXXXXX.

Option 3 — permanently disable encrypted home (if you no longer want this behavior): back up the data, then remove the user's ecryptfs setup and move files back into a normal home directory. This is more invasive — the cleanest route is usually: log in, copy everything to an external location, recreate the account without home encryption.

If the home is not encrypted

If /home/.ecryptfs doesn't exist, then the folder genuinely doesn't exist because VirtualBox only creates ~/VirtualBox VMs (its default machine folder) the first time it's run by that user. In that case there is simply nothing to access — run VBoxManage list vms as that user, or set System › default machine folder / VBOX_USER_HOME to a shared path if you want it available independently of the interactive session.