How do I disable (and re-enable) my Thunderbolt port from the terminal?
Apple has several kexts for the Thunderbolt-Connection :

AppleThunderboltDPAdapters.kext 
AppleThunderboltEDMService.kext
AppleThunderboltIP.kext
AppleThunderboltNHI.kext
AppleThunderboltPCIAdapters.kext
AppleThunderboltUTDM.kext
IOThunderboltFamily.kext 

I think the commands you are looking for are either:

sudo kextunload /System/Library/Extensions/AppleThunderboltPCIAdapters.kext
sudo kextload /System/Library/Extensions/AppleThunderboltPCIAdapters.kext


or

sudo kextunload /System/Library/Extensions/IOThunderboltFamily.kext    
sudo kextload /System/Library/Extensions/IOThunderboltFamily.kext


I have a Thunderbolt port in my Mac Pro, but currently no devices. So I can't tell you exactly which kext does the trick.

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Further Information :

Thunderbolt is basically PCIe tunneled through the DisplayPort Connection. I can imagine that it is based on the ACPIPlatform or IOPCIFamily kernel extension. Either way if you unload those you would probably cut off the branch you're sitting on.

Apple released a document on creating Thunderbolt drivers and how you verify if the device is still online here.

It also says: "In the case of PCI, the I/O PCI family (IOPCIFamily) within the I/O Kit is responsible for enumerating the PCI bridge in the controller chip and any downstream bridges or devices."

Furthermore : "PCI device drivers can determine if a Thunderbolt device is connected by recursively searching over parents in the I/O Registry for the key IOPCITunnelled (...)."

Also have a look into the Developer Library.

Thunderbolt is a complicated technology and you could either write a little program or you can write a launch script that checks and reloads the driver if the device is offline. You could do it manually instead of unplugging it and replugging it in.