Yes, the effect of removing all living things at the trophic level will vary from different trophic levels. For example, if all producers are removed, there is a chance of death or migration of top consumers that will disrupt trophic levels. This is the same on all levels. Therefore, the removal of all organisms at any level can affect the whole environment as the food chain is disrupted. Survival of the fittest animals depends entirely on the animals at the lower levels.
Will the impact of removing all the organisms in the trophic level be different for different trophic levels? Can the organisms of any trophic level be removed without causing any damage to the ecosystem?