Thank you StR. I appreciate you taking the time to try and help me figure this out, even though it's a feature you're unfamiliar with.
On the FAQ page, newbielink:http://www.aqua-mail.com/?page_id=227 [nonactive], under "What is the Smart Folder?", it says the following:
"The Smart Folder shows messages which, over a selectable time period:
1) were sent (this is the date/time in the header);
2) were read, including read in other apps (for IMAP).
3) or are unread, no matter what their date/time is.
You can also include starred messages in this list, please see app settings under Smart Folder or the navigation drawer (side panel) in the smart folder’s message list view.
In other words, this is the list of messages that might require attention, or that you might need to come back to. This folder is enabled by default, but can be disabled in the app’s settings."
I'm thinking that this folder grabbed the original selectable time period I had set up, but is not removing emails that don't fall within the newly selected time period. I'm going to dig through and delete a bunch of emails to see if it starts responding to the newly specified time period.
I'll post back what I find out.