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've ran into the same issue when I tried using the internet connection from my company, either using Application Loader, or Organizer. In fact, the problem came from my company's firewall which was blocking some ports. As it is written in Apple support, you may correct this problem by allowing access to the ports indicated in this file : https://itunesconnect.apple.com/docs/UsingApplicationLoader.pdf from page 6 to 8
I tried to remove these warnings by clean and Archive but could not. Finally I increase the "Bundle versions string, short" in the project's info.plist file and re-uploaded and successfully uploaded the app without warnings.
Upload has received and app is also approved.So i think there is no much problem with this.
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.