I am afraid that when the MoonBot terminal auto-updates, if I have open trades and there are unclosed Sell orders I will not be able to control them, is there any protection against this?

Yes, in order to do this, on the Settings – Autostart tab, you need to check the checkboxes next to: “AutoUpdate the bot” and additionally next to “Postpone AutoUpdate with active sells”. MoonBot will wait until all trades are closed and only then will autorun a new version. This setting does not affect the manual auto-update or the “DoUpdate” command in Telegram.