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Is there anyway to determine whether using Equilibrium has ruined the substrate?
Have you noticed any plants with black, slimy, stinky roots? Maybe you can look through the glass at any roots growing on the edge of the aquarium, or gently pull one plant up a bit to check. From your pictures at least I can see some healthy roots. You could also do some more periodic poking if you're worried. But sounds like things are not extreme enough to warrant tearing down everything.
 
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