Below screenshot is what you will see when update TypeScript 1.5.4 in VS (Tools -> Extensions and Updates -> Updates tab). This message is half-truth. Visual studio will uninstall old version of TypeScript (which is what the message indicates). VS will then install newer version of TypeScript (this is the part that is missing from the message box).
You can safely ignore the message because VS actually correctly install 1.5.4 for you.

Below screenshot is what you will see when update TypeScript 1.5.4 in VS (Tools -> Extensions and Updates -> Updates tab). This message is half-truth. Visual studio will uninstall old version of TypeScript (which is what the message indicates). VS will then install newer version of TypeScript (this is the part that is missing from the message box).
You can safely ignore the message because VS actually correctly install 1.5.4 for you.