I may be alone in thinking this, but I would suggest you stick to the designations of 1L1, 1L2, 1L3, 2L1, 2L2, etc. Then put a note on the front of the DB stating that L1 and L2 are the same supply phase.
It will never be a problem unless someone comes along and tries to add a 3-phase device - and if they can't work out that there aren't 3 different phases then they shouldn't be doing the work.
Just curious, but what made you decide you have L1 and L3? What's to say you haven't got L2 and L3, or L1 and L2?
Does it have a 3-phase meter, or two single phase jobbies?