Lieutenant will not get any bonuses when replacing the General or the Substitute during duel phase.
I'll take this as Lieutenant can't use upped cards if subbing for General, and salvages zero cards when subbing for anyone.
Errr... I'd kind of assumed the General would manage the vault if the Vault Organizer goes MIA, etc. So now the Lieutenant only has responsibilities if both a team member and the General are unavailable, which makes him slightly more valuable than the team's Rookie. If Lietenant can sub for everybody else, maybe we could let him sub for the sub as well?
Also, I hadn't seen the rule clarification in the opening post until kobis pointed it out. If the War Rules undergo even a cosmetic change, posting the rule change is helpful.
The basic idea behind the Lieutenant is that he or she is the person who does things when others fail or go offline. It's a very important job.
General on the other hand has a purely administrative role, and should only try to overlook everything and make sure others are doing their job. For example if the General sees that the team Vault Organizer has disappeared, he or she can order the team Lieutenant to manage the Vault.
Of course these responsibilities are not set into stone. It's just a suggestion for teams that don't have any better plans. Teams can use their own methods if they so choose, for example the General can do all the Vault managing and deckbuilding.
EDIT: I was thinking about letting the Lieutenant use 3 upped cards. It would probably make more sense that way. On the other hand, the event is just about to start and many people get scared off last minute changes