Opening a Popup (modal: false) inside another Popup (modal: true) breaks the mouse wheel functionality of the top level item. The modality of the lower level Popup filters the wheel event out. Changing the modality to false, enables the mouse wheel again.

Suspicion: 

The QQuickOverlay::eventFilter calls for a Wheel::Event the function popupItem->isAncestorOf(topItem) on the popupItem of the modal Popup, which is false if the topItem resides in another Popup. Thus, the EventFilter returns true. This Wheel::Event case is new in Qt6.4.1 compared to Qt5.12.2, in which I didn't run into this issue.

Example:

1) click into green square -> prints: "mouse press from green"

2) use mouse wheel inside green square -> nothing

Expected Behavior:

1) use mouse wheel inside green square -> print: "wheel from green"