I've attached a minimal example that shows the problem,
I constructed it from what we do with the Opt+Tab popup in Qt Creator and which lead to QTCREATORBUG-1665.
In the example, click the "open" button and then "hide".

The widget hierarchy is:

main widget <-- other widget <-- popup widget

where popup widget has flag Qt::Popup.

In "open", popup widget is shown, in "hide" the other widget is reparented to 0 and hidden, and then the popup widget hidden, with the result that the main widget is hidden.
It can't be shown again by clicking on the dock icon, only by cmd+tabbing away from the app and back again. But then, popup widget is still visible, and can't be closed by clicking (which should work since it's a popup).