Any harm in renaming WyUpdate.exe?

After we have built a new updater, can we rename it to updater.exe for example?

No harm at all you can rename it whatever you want and the self-updates will still function correctly. But if you do rename it, it will add extra steps to your build process (because you should always include the latest version of wyUpdate.exe with your app).

I've done this in my application, Universe Sandbox. I renamed it 'update.exe' and it works just fine.