There's already some precedent when dealing with humans reverse engineering systems. We use "cleanroom" approaches where the ones doing the reverse engineering are segregated from those doing the later design and development work. Instead of producing a design document based on the thing being studied, the reverse engineers produce a specification from which a new design, untainted by knowledge of the original design, is produced.
People using ML to try and reverse-engineer and create a "clean" version of things will likely need to use a similar approach. You can't ask one LLM to take in a circuit design as input and produce a specification and design within the same context. The resulting design will be at least partially informed by knowledge of the original design. The way to do this safely (potentially still with suits happening, but safer at least) will be to have one execution to produce a specification, and a second fresh execution taking the specification to produce a design. At least then you know your LLM was not aware of the original design.
Of course, LLM agents "cheat", so you'll also want to be careful to ensure a clean environment if you're using an agent that does not provide access to the original design material.