There's a couple different things you might mean by "reboot".
To reset Teensy, where USB disconnects and your program reboots as if the power had just come up, write to the SCB_AIRCR register.
To reboot to the bootloader, use _teensyduino_reboot_().
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There is no possible way to reset or reboot Teensy 3.1/3.2 in Windows 7 without causing a USB COM port disconnect/disappearance problem described in detail as in the posts linked above, unless using TyQT?
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