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I am trying to export a binary that contains both AARCH64-64 and x86-64 in Ghidra. I only opened the x86-64 counterpart to perform some changes.

When I tried to export it, it exported a .bin file that I can't replace with the original Mach-O universal binary. How do I go about exporting the patched x86-64 as one universal binary in Ghidra?

Original Binary:

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Exported x86-64 Binary:

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This seems like you are effectively running into the same issue as this question: How to export a working elf binary from Ghidra?

Ghidra doesn't export working ELF/PE/Mach-O files when you export something. You have to use an existing proper exporter to get a patched binary. I am not aware of one for Mach-O, especially not Mach-O with multiple architectures, but it might still be possible to write a minimal one for your use case.

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