We are trying to upload an updated version of the app to the store. The upload takes a long time and finally when its done, we receive the following WARNINGS.
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I think you can ignore the warning. People who had that warning have had their apps approved by Apple. According to https://forums.adobe.com/message/5949439 it most probably has to do with version number. Here's a quote
Ignore it. Apple is just letting you know that the version number in the app isn't the same as the version number in iTunes Connect. The iTunes Connect version is what's displayed in iTunes/App Store.