|I don't believe you can in batch without some sort of third party intervention.|
VBScript has SendKeys, so you could use that to emulate keyboard controls.
PowerShell gives you access to a C# compiler, and though that you can access the Win32 API. It's not pretty, but anything you can do programmatically, you can do with PowerShell. This includes finding the buttons in question and sending BM_CLICK messages.
The better question is what are these pop-ups, and what can you do to prevent them from popping up?
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