This TUI utility provides an easy way to copy addon settings, keybinds, and macros between characters, or even different versions of the WoW client (e.g. PTR).
It does not currently copy client settings (graphics, sound levels, etc) between versions of the game.
This software overwrites large amounts of configuration data automatically. There is no "undo". For that reason, before you copy profiles around, you should consider taking a backup.
To do that, simply copy the entire WTF folder in the version folder that you're going to be copying to (e.g. _classic_ptr_) to somewhere safe before running the tool.
Disable keybind synchronization.
Log into the game version that configs are being copied to.
Type this in the chat window:
/console synchronizeBindings 0
Close the game, Re-run the sync.
Open the game, and run:
/console synchronizeBindings 1
In the chat window.
Change any key binding, and apply the changes - you can change it back later.
This "tricks" the WoW client into accepting the new keybindings, and saving them to Blizzard's servers. Otherwise, it sees that the keybindings for the account don't match the ones saved on the server, and "helpfully" changes them.
Leaving synchronizeBindings turned off entirely also solves the issue.