This is perplexing, because iOS ostensibly keeps track of the account to which an incoming email shows up, and uses that as the basis of which email server to use (and which associated email address) for a reply. A message arriving to address A should pass through corresponding server A. When you reply, iOS should “know” this and pick the associated email address.
For whatever reason, that’s not happening. There are two ways you can affect this.
I’ve discovered a few times that legacy email setup in iOS has caused me trouble. By removing an account from Mail, Contacts, Calendars and adding it fresh, I’ve resolved trouble with Apple and third-party calendar software, email handling, and other situations. So long as all your email is stored on a server, removing and re-adding the account won’t delete messages.
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