I just upgraded my production system (Windows Server 2008 R2) to R12, after the upgrade the bin64 folder is empty. I did it a 2nd time, same thing.
I did the same upgrade a couple weeks ago on my R&D machine (Windows 7 Pro) without any problem.
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I just completely uninstalled Ninja, and did a fresh install that worked ok ... There is likely an issue in the upgrade process for 64bit.
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