It doesn't overwrite anything.
What happens is Kong binds your in-game name, whatever that may be, to your Kongregate username.
Linking the accounts merely changes that binding.
If you still know your original in-game name and password, and link back, you will still have everything.
In fact, you don't even need to link it - that'll be for convenience sake.
I "Lost" my account once through linking, and that was how I got it back.