I've just tried to upload a build via command line - as I use jenkins to push jobs up to iTunesConnect - and I too am seeing the error about application not existing. I thought it was because I had not created a new version, but it isn't that. I tried running Application Loader itself (from Xcode 6.4) and it was able to successfully upload the ipa file.
The error I am seeing from altool is:
*** Error: Failed to get authorization token: Error Domain=ITunesConnectFoundationErrorDomain Code=-20203 "The application you have selected does not exist." UserInfo=0x7f8bd146fdb0 {NSLocalizedDescription=The application you have selected does not exist., NSLocalizedFailureReason=Unable to validate your application.}
This has worked previously, and I was certainly able to use it on Tuesday without error.