That appears to be the current behavior of the iPhone software with Exchange Activesync.
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After replying to an email on my iPhone the email in the Exchange account through Outlook doesn't show as being replied to.
3 replies
Look in your sent items folder.
I've noticed this as well, somewhat irritating. The 'reply' items do show up in your sent folder, but the message you replied to isn't shown as 'replied-to' in Outlook. Seems like a bug with activesync.
iPhone email replies don't show as replied to on Exchange account