Returning agents to pool in in Waterdeep Harbor phase
Yes, you can reassign the returned agents; you do so immediately before continuing with the Waterdeep Harbour phase. But no, you cannot place them in the Harbour. From the FAQ:

Q: If I complete the &quot;Recruit Lieutenant&quot; quest as a result of reassigning an agent from &quot;Waterdeep Harbor&quot;, do I get to assign that agent immediately?

A: Yes. If any effect puts a new agent into your pool during reassignment from &quot;Waterdeep Harbor&quot;, you assign that agent immediately. However, you can't assign him to &quot;Waterdeep Harbor&quot; (he follows the same rule as the &quot;Research Chronomancy&quot; quest, a returned/new agent can't be assigned to &quot;Waterdeep Harbor&quot; during the reassignment phase of the round).