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If there are lots of live maggots that probably also means their are unhatched eggs too. Yes, your culture does have a chance of recovery but it might take a while. If you are able to introduce more adult flies that would help greatly.

 
I’m wondering if there’s a way to prevent the filter from directly contacting the medium so it can’t absorb moisture from it.

 
While you could do that the main reason for the filter/excelsior is so the flies are able to climb to and from the medium without getting stuck so it really needs to be touching the medium.

In the case of the filters they would eventually collapse when they absorb too much moisture and keeping the filter away from the medium doesn't solve the issue of them being weighted down with flies. The only way I see to solve the problems with using coffee filters is to make the medium a little drier & see if you can find thicker sturdier coffee filters.

I once bought a culture that used green plastic mesh and that seemed to work okay but not optimal. The medium didn't stick to the mesh at all so I had to keep pushing it down into the medium to maintain contact. This pic was taken right after it arrived in the mail, the mesh was still pushed into the medium but because the mesh was springy, the medium was kinda watery and I would tap the container while getting flies out, the mesh would retract over time. It would stay pushed down for 4 or 5 days before coming out again. Maybe this issue could have been solved by making the medium thicker and less watery.

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...Of course you can just use excelsior. It works really well and why fix something that isn't broken? 

 
It's ok, making mistakes is how we learn. I don't mean to discourage you from experimenting, who knows you could eventually discover something that works even better! However, an experiment needs a control group to compare against to see if it really is better or not. The control doubly serves as backup insurance should the experimental culture fail. Good luck with your experiments, the water cup thing sounds interesting.

 
When in doubt, I always check to see what the dart frog guys do:

Fruit Flies: Coffee filter vs. Excelsior

One person writes, "Another advantage to coffee filters, BTW, is that they suck up excess moisture in the media, and slowly dose it back out in the course of the culture's life, and so I've found that cultures with coffee filters don't get as dried out near the end of their production."

 
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One really great tip I got from DeShawn. He said to use Repashy Superfly medium. It works better than any other commercially available medium, it produces more flies and they actually use up all the culture by the end of the month making it worth the money. I can see a huge difference in my yields now, the maggots and pupae end up on every surface in the cup and the excelsior, I actually had to make another culture because there were too many flies in there at one point.

 
I make my own and always have, I have more flies than u can shake a stick at!
Do you mind sharing the recipe or do you have the medium for sale on your website? 

I've tried several commercially available fly mediums and a couple of simple recipes I found online and almost always had similar results, the last one I tried from Josh's Frog's also left tons of medium unused at the end of culture. Repashy surprised me at how well it works, it made me realize I was only getting mediocre yields of flies before. It was enough to feed the mantises I had at the time so that's not really a bad thing but now that I expanded my collection and have several ooths due to hatch soon I need something more productive. The other alternative would simply be to make more cultures but that seems like a waste of medium and space if I can accomplish the same amount of flies in one deli cup with Repashy.

 
Do you mind sharing the recipe or do you have the medium for sale on your website?
Once again, from the frog folks:

Best Homemade FF Media

.......Pretty much all the media sold in the hobby is one form or another of what is referred to as the "carolina biological supply mix".  They are variations of what is used in labs to raise fruit flies.......

.......the simplest media recipe is based on nothing more than potato flakes, brewer's' yeast (dead), confectioner's sugar, a mold inhibitor and water. This is what is commonly referred to as the "carolina biological supply" recipe. It is the industry standard and is used in fly labs around the world because of it's reliability.......

 
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I make my own media and use 5 coffee filters. The filters do tend to slowly sink down with the weight of the hydei (mel cultures rarely have this issue). Usually about mid way through I just add 2 additional filters for the adult flies to climb on. Despite how it looks the maggots don't seem to have a problem getting around the sunken ones and pupating. Not saying a certain portion of the yield isn't lost, but I've always produced way more than I need. At one point I tested things like a small cut off plastic cup for the filters to rest in so they weren't laden with moisture. It was the worst producing culture I ever had. I think the moisture drawn up helps keep the pupae from getting too dry as pupae will often cover the filters.

I remember seeing someone had a lot of success with cotton balls so maybe sticking some on the bottom might help keep the filters form drawing up so much moisture? I'll admit I've been pretty lazy with testing things out because I produce more than I need with ease so I've adopted a bit of if it ain't broke don't fix it mentality.

 
I personally have never got around to finding excelsior, so I've tried a other options. With the coffee filters, I had good results, but they tended to collapse if the media is too watery.  I like to use the more rigid cone shaped filters, since they can't collapse. I also like to use pieces of paper plates jammed into the substrate. They work great, and they never get too soggy.

 

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