I know that this might sound a bit weird, but I think that cats pick up our moods, as they are very sensitive regarding their surroundings...could it be that Luna has picked up your mood, being a bit unsecure at the moment?!
Maybe she feels the stress the same way you do and seeing you unhappy makes her feel unhappy, too!?
Maybe she has felt this before at the time when you've inteneded to take Lily in and wasn't sure wether it worked out with Luna and you've been worried?!

I know your current situation isn't very supportive but try to be positive when Luna is around and try to not worry so much about the two sweeties...

As for a health reason...could it be that Luna instead of having her special diet only also eats from Lily's food?!

If you have a gut feeling that it's a health issue, you should have her checked again!!!

However: GOOD LUCK!!!