I ran into the same issue a couple of days ago and I am currently still trying to find out what went wrong. As the "Update Code" function did not work i tried the following steps:
1. delete the app from phonegap build
2. create the new app by uploading the application zip file
3. click on "Ready to build"
However the build of the application does not seem to work as it hangs ( displays the loading animation on the button ) but does not finish building.
* I tried building with pg cli version "cli-6.3.0" and also tried it with "cli-5.2.0"
* Once the build tool finished building with the error "index.html not found"
Any information would be appreciated.
I am in the same situation
Using a different tool for creating the zip file did not work for me.
I finally managed to solve the problem by deleting the app and creating it again with a new upload ( see Re: Error: upload failed; please try again  ). Since then all my problems disappeared.