Now I'm confused. 
A08 was released 9-Nov'12, so there's a reasonable possibility that your system had A06.
If you actually went from A06 directly to A09, you may have damaged the motherboard and it does have to be replaced. There is a notice on Dell's NL Support site saying, in English: "You may run A09.exe if you are already updated to A08 BIOS." When all else fails, read the instructions! 
On some Dell systems, you can flash back to an earlier version of BIOS than currently installed. The instructions for A09 on the XPS 2710 say there's no going back to an earlier version. So if A09 "breaks" something that worked correctly in A08, you'd be stuck. That's why we only recommend doing a BIOS flash update if the update fixes a problem you actually have, and/or Dell says the update is "recommended or "critical".
You shouldn't have any issues using the existing installation of Windows and software on the hard drive with the new motherboard. There shouldn't be any copyright issues. At the worst, you might have to contact Microsoft to validate the new key that's stored in BIOS, but that shouldn't require anything more than entering a code they'd provide, perhaps via telephone support.