Great detailed analysis in the backtrace! :) What confused me at first was that the present_wnmd_flips_stop function is called at all in this state because it should only be called when at least one flip has been done and in this case xwl_window->present_window must have been set to the presenting (child) window.
I believe now the root problem is that the window did in fact some flips in the past, but on the reparent operation a new parent window with a new xwl_window struct is set, which then has a different present_window value. That means when reparenting of a child window with flips the xwl_window->present_window values must be updated on the old parent (to NULL) and on the new parent (to the new child window). Or more generic this must be done on any unmap/map operation. One extra case must be considered: if there is already a different child window doing flips on the new parent window the reparented child window must be instructed to stop its flips.
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