The report is not clear, but I just realized there's indeed a bug, at least on my Debian Stretch GTK 3.22.11, Adwaita theme: if I resize the pane handle far enough to the right of the window, contents of the whole paned starts to move up -- and thus disappear off the top. This is however related to the window size as well, if I resize the window to be wider, the contents moves back down, so it's not a mere absolute value.
This doesn't look likely to be a strictly Geany bug but more probably one in GTK somehow, but I might try to investigate it a little.