Moo

[Willito]

Here's a stab at it. I think it's a combination of things changing all around the same time.
Eliminating the sand - releasing toxic nitrate and loosing buffering abilities
Blasting rocks (with freshwater I assume) - killing off vast amount of denitrifying bacteria causing a biological imbalance. Also killing whatever'ss living in/on the rocks causing more decay.
Missing cucumbers - dead, possibly releasing toxin
Large water changes - perhaps too large volume, too frequent

If you combine all these changes together, and assuming that's what took place, it becomes a very different environment for these delicate species to cope with. I don't believe changes to the aqauscape or the lack of corals contribute to their rapid decend. Lets hope whatever still swimming can cope in the new setup.