Dolphin 4.0 uses a global user directory now for all OSes: https://wiki.dolphin-emu.org/index.php?title=Controlling_the_Global_User_Directory
Your controller profiles should now be in My Documents\Dolphin Emulator\Config\Profiles iirc
EDIT: If you're using an older revision of Dolphin, you might have to look in your old folder and copy+paste the profiles into Dolphin 4.0's global folder.
Your controller profiles should now be in My Documents\Dolphin Emulator\Config\Profiles iirc
EDIT: If you're using an older revision of Dolphin, you might have to look in your old folder and copy+paste the profiles into Dolphin 4.0's global folder.