I too have windows 8 installed on a SSD drive and did not want my everyday user profile to take up space on the speedy drive, so I changed my profile to work off of my normal drive where there was pretty of room. I noticed when they release windows 8.1 preview, that the upgrade would not work and the reason for this was due to my "user profiles" were not in the default location. So I waited for 8.1 final release and just figured they would resolve this issue...but know, they didn't. So, here is how I did the upgrade without losing data or installed software.

1. The first thing I did was to copy my everyday user profile off the drive and onto the server (just lucky that I have one...for those of you who don't have one, you could use a flash drive).

2. I then edited the registry to reset my profiles back to the %systemdrive%. See the pic. The pic points to my new profile location and not the SSD drive. Click image for larger version

3. Anyway, just change where ever it says J: back to %systemdrive% Pay close attention to colon and typing before you save. Make a backup prior to making changes would be helpful. Also, never change the ProgramData entry as it should always point to the installation drive.

4. Reboot and log back in with your normal user account (I'm assuming this is an admin account), then create a new admin account with administrator privileges.

5. Now logoff of your normal account and logon with the new admin account you just created in step 4. Verify that this new users profile was created on your SSD drive in the original location...normally c:\users

6. Now go delete the old user accounts and any other unused user accounts.
7. Now that you have changed everything back to what it should be…you should be able to go to the Store and upgrade your computer to 8.1. Once the upgrade has been completed…several reboots later. Logon on with your new admin account that you created in step 4. And make sure everything is working.
8. Now, go back into the registry and change the ProFileList back to your other drive, like I did. As you can see from the image that I’m using j:.
9. Reboot and log back in still using the new admin account. Now create your new user account and make sure to give it administrator privileges (if you are the administrator). Once you have created the account, logout and log back in with the new user you just created. Then verify that this new user profile was created in the drive that you specified in the registry. IF so, then you did it right and your saving space on your SSD drive.
10. Now copy all your data back from the location you copied it too. And all your data will or is restored and all of your applications will work. I know that when I clicked on an excel document, excel popped up a window as if it was the first time it had been used, but worked perfectly.
11. With some of my applications I did have to re-register them but I did not have to reinstall them. Most of them worked like nothing had changed.
Anyway, here’s hoping this helps someone with their upgrade, good luck and enjoy!