I know this is a newbie question, but...
I have not updated my watchApp for around three months till I tried today and get "Signature check failed. All app versions have to be signed with the same key pair."
The App ID is the same on the new file as the existing file.
I can see the id on the existing app in the App Store: Manifest AppID: 5351ff702e074b5f82bb2fcafd377add
and on the update it's:
<iq:application entry="main" id="5351ff702e074b5f82bb2fcafd377add". character for character the same.