The short answer: it shouldn't, and we go out of our way to make sure it can't.
Every destructive command pauses for your approval. Read-only commands (looking at files, checking service status) run automatically, but anything that writes, deletes, restarts, or installs shows you the exact command and waits for you to click Yes. You always see what's about to happen.
Files that get replaced are backed up. When the Files tab overwrites or deletes anything, the previous version goes into a .helm-backup/ folder next to where it lived. Recover it from the Trash panel in the same Files tab — see Backups: which one do I want for the walkthrough.
SSH credentials live only in your session's memory. They're never written to disk on Server Manager's side. When you sign out or close the tab, the keys are gone from our end.
Disconnecting Server Manager doesn't touch your server. The sites and services on it keep running as configured. Server Manager is a control surface — it isn't a runtime your apps depend on.
If Faro ever proposes something irreversible (deleting a database, wiping a deploy folder without backup), it warns you explicitly and asks twice.