If updating from version 1.0 only then please refer back to the email that you received from the Flight Sim Store as some additional checks are required.
The recommended Update Procedure is to uninstall and then install the new version as follows:
Uninstall the libraries using the option in DX10Controller
Open Control Panel/Add or Remove Programs and remove SteveFx – DX10SceneryFixer
Launch the downloaded FSS Installer for the new version and follow the instructions, reentering your key if necessary.
Launch DX10 Controller and Install the libraries
Read the Manual!
Note that the 1.4 FSS Uninstaller removes the directory containing your profiles – if you want to retain them please copy them elsewhere before starting the uninstallation process.