Hello Ed,
Yes -- in any Hauptwerk version (v2-v6) simply ticking/enabling a MIDI port (whether MIDI OUT or MIDI IN) won't in itself lose any settings. (In v2-v5 the important thing is that you don't un-tick any of the ticked entries, since doing so would clear MIDI settings that related to them.)
It's also always good practice to use 'File | Backup ...' before changing anything anyway, so that one can get back to one's current settings if ever needed.