AquaMail, K9 Mail, stock Android Email, Mail Droid, Kaiten, Gmail, and all other mobile mail apps --
-- only keep up to date (sync) a limited amount of recent messages per folder, not all (potentially thousands, or hundreds of thousands of messages).
And if you need to see older messages beyond that, just scroll down and the app will sync more messages into view.
No change there.
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What is different in this version and only for Yahoo accounts:
If you have let's say 3 unread messages within those 25, and 10 older unread messages (older, beyond the "25 message window"), then the unread counter will say 3, not 13.
So you'll still see when you have new unread messages, but not that there may be older unread messages.
And BTW, this is how the unread counter works in stock Android Email and K9 Mail, so it's not "wrong", just different from how Aqua normally shows the number of all unread messages, both new and old.