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.