I've done this using the http://www.nexusmods.com/skyrim/mods/52363/? and Mod Organizer. MO minimizes the risk if it didn't work out. I've done this to at least 2 profiles and so far it worked for me. Here's the procedure I used:
1. Use MO and made a copy of the profile I want to switch from UFO to AFT.
2. Start the game using the new copy of the profile.
3. Dismiss all followers.
4. Find Tina the Firefly in Riverwood and stop the mod.
5. Make a new save. Quit.
6. Uninstall UFO.
7. Resort the loader with LOOT. Load game. Wait a bit and make a new save. Quit.
8. Open the last saved game in save game script cleaner.
9. Clean the file according to directions.
10. Load the game with cleaned save file. Make a new save file. Quit.
11. Install AFT. Resort with LOOT.