Just trying this myself, as an owner of a 4.5.1 licence.
You can read at http://blogs.adobe.com/flex/2011/11/flex-4-6-and-flash-builder-4-6-updates-now-available.h tml that "Flash Builder 4.6 is a free update to Flash Builder 4.5".
FB4.6 wont install if 4.5 is installed, so I uninstalled 4.5, ticking the 'deactivate' box.
The FB4.6 installer then runs OK, and took my licence key fine (even asking for the licence key for the version I upgraded from correctly).
Yes, if you mucked with the SDKs in the install folder, you'll need to do it again. I create copies in another place when I add AIR to save this pain, for instance. You should be able to copy them out before you uninstall though.
Thanks. It took me quite a while to get 4.6 installed.
I uninstalled 4.5(.1) but got an error anyway when initializing the installation of 4.6
Then I tried uninstalling Adobe Air from the utilities directory under Application as described in this thread
That didn't work either.
Finally I uninstalled Flash CS5 as well as my complete CS4 suite. I am not sure if only uninstallng Flash CS5 would have been sufficient, maybe.
After this I sucesfully installed Flash Builder 4.6, and then re-installed the CS4 suite and Flash CS5.
The only problem left is that when I create a new project and compile, I get a java.lang.NullPointerException
but I will post that in a new thread...