how to change version number of an App from iTunesConnect with state Prepare for Submission

You can update the version name in a version field in the General App Information area. Screenshot is as below

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I have the same problem before.

My solution:

Submit the IPA first, status will be changed to "Waiting for Review";
Press the red button "Reject the binary" in iTunes Connect, status will be changed to "Developer Rejected";
Restart the process again.

UPDATE As of 2015, iTunes Connect has updated, allowing users to change version number without uploading any binary.

Go to iTunes --> App store --> iOS App at left side --> Prepare for submission --> General App Information --> Version

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