Both the sand and the repti-bark can become impacted if eaten. I would get rid of the substrate. Most of our members use either paper towels or newspaper as something really simple. Its clean and won't have any strange things in it. The moss is actually something that can breed bacteria as well as bugs. A folded up moist paper towel is good for them.

Here is our care sheet.
http://reptileguides.herpcenter.com/...122.html?t=122

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My name is Liz
Do what's best for the animal, not what's best for you.

Please give us a total rundown on how the gecko is being housed. As much detail as possible. There is a lot of bad information out there and we may be able to pick something up that could be a hazard and has been overlooked.
The reason the gecko hides all the time is, it is nocturnal. They sleep during the day and move around at night. If you look in on him after it gets dark you will be more likely to see him out and about. The fact that the mealworms are disappearing shows that the gecko is eating.
Have you checked in the hide for feces? That may be why you have the flies in there.
Is the moss long fibered sphagnum or is it sphagnum peat moss. One is long and stringy and the other is ground up and looks like soil. What you need is the long fibered type.
I personally would get rid of all the substrate and replace it with simple newspaper or paper towel. The particulate substrate poses a danger of being consumed resulting in the impaction of the animal's digestive system.

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Merlin,
What's Life Without A Little Magic!

The Leo is in a huge viv as was once used for a fully grown cornsnake. it has 2 logs, a food, water bowl, a large exo-terra cave, medium exo-terra snake cave with the spahgnum long fibered moss, it has a cacium dish in it. it has a red 40w light and a heat matt, i keep the light on all day along with the heat matt which keeps the viv at around 80-85 and I have just the heat matt on at night which keeps the viv around 70-75. i could take a picture or 2 if that would help.

When you say huge, how big of a viv and how big is the gecko? Also, did you clean the viv real good before putting your gecko into it after the corn snake?

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MARSHA
A man without a woman is a bachelor, A woman without a man is a genius!.

We have enough youth, how about a fountain of smart!

Yes I Cleaned it thourughly the viv is 35" long, 15" wide and 16" tall
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I would ditch the red light and get a regular household light bulb so it isnt so dark. I would get rid of the substrate also as Merlin stated. That isnt appropriate for a gecko. Simple papertowel, shelf liner, tile, or reptile carpet would be better.

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MARSHA
A man without a woman is a bachelor, A woman without a man is a genius!.

We have enough youth, how about a fountain of smart!

its not that dark its just a dodgy camera

What Marsha is getting at is there needs to be a simulation of daylight and night. The brighter day is when the gecko will sleep. The darkness of night is when it will be up and around.

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Merlin,
What's Life Without A Little Magic!

well the room that I house the gecko in gets alot of light anyway but I will give it ago and see what happens, thanks for your help