I have been dealing with this issue for a while now and like the title says 'Thunderbolt Doesn't Survive Restart', a more accurate description would be, "Thunderbolt No Longer Activated After Shutdown From Mac OS".
Shutting down the computer from Sierra, kills thunderbolt activation from Windows. But shutting down the computer from Windows, does not.
If you shut down from Mac OS, you have to go into windows to get your thunderbolt working again but you don't have to restart and go into Mac OS right away, you can shut down from Windows and Mac OS will have thunderbolt next time you boot up, without having to go into windows but thunderbolt will stop working as soon as you shutdown within Mac OS and has to be 'activated' by windows again.
This could mean that something in the hackintosh is killing thunderbolt activation on shutdown from Mac OS. Could it be a power issue, or shutdown issue or kext issue or something else? I have not tried holding down the power button and not shutting down Mac OS properly since I'm running it of an SSD and that could cause big problems but if thunderbolt did still work after doing that, then we know the issue is due to something happening at shutdown in the Mac OS.
Not everyone has the 'legacy' option for thunderbolt in bios, it's not present in almost all laptops which have thunderbolt, which is increasing all the time. It would be good to find a solution to this.
