Non-Blue Juice is typically used in aircraft like BE40s that have aft lavs and are suit-case type that you ahve to carry through the cabin to dump. The use of non-blue juice is so if any drips on the carpet, you won't see a big blue stain.
I assume you have a lav that is servicable externally. 1st, always make sure you have the proper amount of fluid going back into the unit. You can tell that by how quickly you see water when it is flushed. When you flush it, water should appear right away. If there is even the slightest delay, you do not have enough in there. That's the 1st step in ensuring the smell stays away.
As for getting rid of the smell, get some scalding hot water and fill the lav with it. If it normally takes 1.5 gallons, put in 2 gallons. Pour the scalding hot water directly into the toilet. Now flush it 4 or 5 times and dump it. Repeat that process 2 or 3 times.
Now, get some more hot water and add bleach to it. Put the same amount of water in there and pour a healthy amount of bleach in behind it or premix it before you pour it into the toilet, it does not matter which way you do it. Flush it 4 or 5 times and leave it overnight, but not longer than about 12 hours max. Power the plane back up flush it once or twice and dump it. Now add your regular fill and it should be good to go. If smell is still there after all that, then you might have a leak somewhere from a frozen line or something of that sort.
As for leaving the lav empty I would only do that if it is possibly going to freeze. Otherwise, you should have an additive in the lav water that eats bacteria (what turns the water blue), so leaving it in there does more good than bad. If it has been idle for a few days just service the lav before your flight. Good luck.........
