Better chances are that it won't even boot. Amd and intel chipsets, drivers etc are nothing alike. It will require a fresh install of windows with the new motherboard and cpu in order to function. Currently your existing os setup is configured with drivers for the 990fxa, when you go to boot windows it's going to begin initializing all the instructions for the specific hardware on the 990fxa. When in fact the z97 motherboard is in place it's going to have a severe mismatch of hardware/software. Not that it will damage anything but it will just give up and fail to boot.
Best to backup any important data/files, format the hard drive and do a fresh install with the appropriate drivers and then reinstall programs and copy back your personal files. That way you're sure not to have any mess involving outdated/incompatible files that can cause problems down the road.