If you don't like how Thunderbird indicates a folder has new mail you could add something like the following to a user file in the chrome directory in the profile to make it easier to see which folders have new mail.

The Advanced Folder View list box on top of the folder pane defaults to "All Folders".

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It can be set to "Unread Folders" using the left or right arrows.

This will display only folders that Thunderbird knows has new messages.

It "knows" about any new messages stored in POP accounts or Local Folders, any remote folders that you've opened, and any remote folders that its configured to check for new mail in that folder.

It doesn't know about any new messages in webmail folders unless you used a webmail add-on and checking for new mail downloaded them to the Inbox folder.

It took a while to set up, due to the interface my email hoster uses, but it works like a charm.

The only annoyance was that Thunderbird only ever synced my main Inbox folder, not all subfolders.If I am viewing my Inbox folder and switch to my Sent Items folder nothing changes until I mouse over the entries then they disappear as I move my mouse over them, as they get highlighted.The Empty star icons remain, this might just be a default displayed in the message list pane.You've deleted a message weeks ago, you're certain, and it still shows up in a folder?Sometimes, Mozilla Thunderbird folders' appearance loses track of the underlying structure: messages actually present are not shown, or deleted emails still present.The Extra Folder Columns add-on restores the Unread, Total and Size columns in the folder pane that Thunderbird used to have.