This was infuriating but solved it, it takes a few tries but it works. This is what I did:

1. Open Safari

2. Have a look at the exact position of the “Keep Both” button (or maybe the other one, I didn’t test)

3. Move your mouse to that exact location. Observe: you can’t click anything in Safari

4. Press Option-Command-ESC to open the Force Quit dialog. Don’t move the mouse

5. Use the keyboard to select Safari. Don’t move the mouse

6. Press Enter / Return. Again, don’t move the mouse

7. Press Command-Space to open Spotlight. Again, don’t move the mouse

8. Type Safari and get ready to press the mouse but don’t move the mouse

9. Press Enter and press the “Keep Both” with your trackpad at the exact instant it appears. You’ll need to be quick.

10. If you missed the button, repeat steps 3 through 9.