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When I exit HONK, it asks me if I want to save before closing. Whether I hit "Save Changes," "Discard Changes," or the little "x" to the left of the popup, I can't proceed unless I completely shut down the program.

Have you clicked off the window? I was facing the same issue, but that was because I had the HONK window selected. If you choose a different window, it should track. Hope this helps!