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I would air out those jars to release some of the gas and condensation build-up. The environment should be humid not dripping with water. You could keep the lids cracked just slightly.
Remove any dead plant material.
Hopefully you will get advice from others about their DSM experiences. I only did it once.
I hope you did not put the plants in full sunlight without adjusting them to the intense light. But if the plants are doing okay by now--two days later--then you're fine. (I almost cooked a magnolia sapling after transferring it from heavy shade to a sunny garden spot. Leaves turned brown overnight!)
Looks like a fun project and I wish you luck!
 

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Your tank setups look really nice, and I detect an investigative inquiring mind. I suspect that you will add water to one jar at a time. See how it does and proceed from there cautiously.
Hope you and your jars will ride out the storm. Here in NC, it's the hurricane aftermaths that bring rain to break summer droughts, so they are welcome.
 

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Crypts take awhile to adjust, so its not surprising that yours melted. The Crypt was probably in the emergent form when you bought it. Now it must convert to the submerged form. If the root system is strong (lots of stored carbohydrates), it may do fine.

Your soil is decomposing fast and has made the substrate very anaerobic. You don't have any water circulation in the bowl, so bowl probably has an anaerobic water layer over the substrate. Note, the setup I've described in my book always involved a large tank with some kind of filter or water pump. That brought oxygen near the substrate and counteracted the potential problems you are describing.

I'm not saying you need water circulation or aeration, but you'll need to counteract the lack of oxygen somehow until the soil "settles down."

Yes, poke the substrate gently with very thin object (opened paper clip) so as not to injure roots. Keep up water changes. If anything, the associated water movement with these activities will mix the anaerobic layer above the soil. The presence of all the animals suggests that there's a banquet of nutrients here. :)
 
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