systray notification indicates new mail despite me deleting all messages from another client
I use gMail and IMAP I've had this issue for years. When I delete a message from the inbox on another client - say my phone or from a web-browser, most of the time, the systray notification says I have new mail despite there being no messages there.
I can go to the inbox to confirm that it's empty. When I switch to another folder then back again, the Systray "New Mail" icon will then go away.
About 20% of the time the icon will correctly update itself.
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It takes time for various devices to update changes to IMAP folders. I've seen it take 2 seconds, or a minute. I notice particularly that my smartphone can take a long time before it shows changes that I make in Thunderbird to IMAP folders.
Sometime between showing the systray notification and you opening the Inbox in Thunderbird, then change happens.
You can turn off the systray notification for Thunderbird new e-mails, if it bugs you. I've done that myself, and I rely on a sound playing for notification of new e-mails.