Hi Peter1, notr sure if I understand you correctly but here are my thoughts on it:
I upgraded from Vista to 8.0 while I could still do so for £25, and it gave me a new product key (Windows 8) which I used.
When it came to 8.1, I downloaded the ISO and tried to install using that, but it was no good. I'd read online tutorials on how to get it to download, which was successful, but when installing it the wizard asked for my licence key. I typed in my W8 one, but it wouldn't take it. I did this three or four times to be sure it wasn't down to a typo.
So I then used the store to download 8.1, and it gave me a new product key which I had to use.
So if you're upgrading from 8.0 to 8.1 via the Windows Store, you should have no issues.
The other thing to check is whether you're legally allowed to use that key for another install on another machine … are you installing 8.1 onto another box or the same one so you get a clean install?
Windows 8.1 is installed as en entirely new OS by the looks of things. If you go to Disk Cleanup afterwards and choose the option to remove previous versions of Windows, you'll see that your old Windows 8 installation can be removed (which frees up quite a lot of disk space).
Of course, before upgrading your OS, be sure to back all your data up so if anything does go wrong, you haven't lost anything.