I discovered – too late – that deleting a conversation thread from the Inbox also deletes all the sent mail in that conversation from the Sent folder. This is not what I want. For me, sent mail should always remain in the Sent folder forever so that I can verify that I actually sent an email to somebody.
Is there a setting I can tweak to change this behavior?
It really depends on what you want to do.
To delete a conversation, select it, and click on the delete icon, toolbar button or keyboard Del key. That will delete the whole conversation, so all the messages in the conversation regardless of what folders they are in.
To delete only some messages in a conversation, expand the conversation thread, then select the message and delete it by clicking on the delete icon, toolbar button or keyboard Del key.
Or you can right-click in the body of the message you want to delete, and choose Delete. You will need to use that method if you have a Free license, because you won’t have the thread view,
If conversations don’t work for you, you can disable them using Menu > View > Conversations > DIsable Conversations.
Thanks. That’s very clear and helpful. Sounds like you’ve fielded this question before. 
For the record, this still isn’t the behavior I prefer. For me, the iOS Mail app does it correctly. It shows conversations as threads in the Inbox (if you enable that feature) but deleting such a conversation does not delete anything from the Sent folder. This clears your Inbox while leaving a record in the Sent folder. For me, that’s the ideal behavior.
