If your app has been rejected, you might have to rebuild your app and submit the new ipa file with the application loader. If you subscribed to Apollo Apps takes care service, our team we'll do it for you.
Once you've sent the new ipa file on iTunes connect, you must delete the previous one rejected by Apple.
Go to the menu My apps, click on the app rejected, then click again on the iOS version refused.
Mouse hover the ipa under the part "Build", to delete it, click the icon next to the ipa file previously downloaded.
You can now add your your ipa file by clicking + that is now showing next to Build.
Make sure to choose the last ipa file with your last modifications.
All you need to do now is to save your modifications and submit your application again.