Yeah, looks like the soil buffering ability is exhausted. The use of RO/distilled water actually lengthens the buffering ability of the soil (as the soil doesn't have to work as hard to maintain lower pH), but it all still depends on the actual buffering lifespan of the soil, they will expire eventually. Btw, what soil are you using for your shrimp tank?
Anyways, to change the soil, you will just need to transfer and acclimate all the shrimps out to another temporary tank (it should be fully cycled beforehand with the same water parameters too), then remove the old soil and replace it with new soil. Let the filtration run for a few days to cycle the tank again (it should be quicker since you are using mature filter). Once you measure the tank parameters are stable and safe, then gradually acclimate and transfer the shrimps back into the tank.
To make things easier next time, consider putting the soil into a container or smaller tank which is then put into your main tank (its a sort of modular setup), the rest of the tank can be barebottom (or just a very thin later of substrate for decoration), that will make it alot easier to remove and replace the soil in the future.









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