if you connect your midi controller e.g. over qjackctl
and not over the h2 prefs you lose your connections if you restart the driver or restart hydrogen.
imo, the h2 pref dialog to handle the midi connections is not really useful to do this. because with this dialog you can not connect more than one device.
i use mostly two. my bcr2000 and my master-keyboard. so i have to reconnect one of the controller for each session. also it would great if the h2 dialog recognise that there are connections, if you handle them in a other way, store this into the references. maybe only temporally for the current session.