I'm not familiar with having QTP reboot a machine, but I believe you can use a System Test in Quality Center to reboot a machine. There are a lot of tricks to make it work (mostly regarding getting the machine logged back in after the reboot), but the Quality Center user guide explains how to use it.
So instead of having 1 QTP Test do something, reboot, and do something else, you'd have 3 tests...
QTP Test 1: First part of original test
System Test: Perform Reboot
QTP Test 2: Second part of original test
Then set them up in the Execution Flow of a test set to run one after the other.