Can I set the reply-to conditionally in my Mailback Emails using an element?  

Here is how it works:

1. Create an Email field and in its advanced tab, check "Mailback"
2. Create a list that the user has to chose from. Give it some values as you like dept1, dept2 (but no Email addresses)
3. Now go form => advanced => more options => Mailback Emails => Alternative From Email => add this

{NAME-OF-SELECT: dept1 > department1@company.com, dept2 > department2@company.com} 

Replace NAME-OF-SELECT by the name of the select list (or radio group, if you prefer this) and use its values to determine on what selection what Email should be addressed (like in the example above).

This would cover Mailbacks, so the users can click "reply" in the Email clients and answer to the right receipient.

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For the administrator (or better those who should get their own users), it is almost the same:

Go to form => advanced => more options => Admin Emails => Email Notification => set to "Custom Address" => in "Email to", add this:

{NAME-OF-SELECT: dept1 > department1@company.com, dept2 > department2@company.com}

This time, instead of just presenting reply-tos in the browser, the emails will actually be _sent_ to the Email addresses given.

Of course you can additionally change the Alternative From Email just like for Mailbacks to show different reply-tos if required.