I opened my flyout to mark a talk page notification as read, the orange "You have new messages" changed into a plain "talk", causing the open flyout to jump right and I missed the button I was trying to click on.
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More to the point, though, this is going to be a bit complicated to fix, because the popup is positioned relative to the DOM element. When you've read the talk page notification, it removes the DOM element, which moves the entire top user toolbar, which in turn moves the popup. We'll have to come up with some creative way to either delay this or stick the popup where it is.
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We could wait until it closes and then adjust the text? That might still causes issues with the user page link jumping. We could also not touch it at all and just wait until the next page view for it to go away? That was the old behavior iirc.