Perhaps you're saying that you've explicitly compiled your application for x64 rather than AnyCPU? I'm not aware of any reason to do that-- using AnyCPU ensures that your app will run on both 32bit and 64bit computers, and I'm not aware of any downside to using it vs. limiting yourself to x64.
If there's some reason why targeting only x64 makes sense, please do share it.
Recompiling all FiddlerCore DLLs and their dependencies to target only x64 would be a non-trivial amount of work. Unless there's some compelling reason to do so with which I'm not yet familiar, I would only be likely to do this work for a commercial license holder.
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