Wine doesn't actually reboot the system, nor does it need to. Close all running Wine processes and the next Wine app you start will do a few things that emulate the Windows boot sequence. Of course, if that boot code somehow crashes Wine and basically makes it unusable, you'll have to start over with a clean wineprefix. You might not be able to install this application properly without breaking Wine (though I have no experience at all with said software) unless you apply special hacks somehow.
