Launch the game through the updated executable. To help you further, could you let me know:
Execute the .exe file within the extracted files, directing it to your game folder. File: NEKOPARA1.18.zip ...
Find your original Nekopara installation folder (usually within your SteamApps folder if bought on Steam). Launch the game through the updated executable
Nekopara_v1.18.exe (or similar file to update the base game). File: NEKOPARA1.18.zip ...