Yes, the impact of removing all organisms in a trophic level will be different for different trophic levels. If all the producers are killed, it will cause death or migration of the primary consumers in the ecosystem.
In the absence of producers, subsequent level of consumers will also be affected. But if primary consumers are removed, organisms of higher trophic level will die, while those of lower level (producers) show exponential growth much beyond the carrying capacity of the environment. Removal of the organisms in a trophic level will upset the whole ecosystem as all categories of organisms are linked through food chain. The survival of organisms of one trophic level depends on the existence of the members of other trophic level.