I tried to find the problem component of that... When I try to delete icon from /usr/share/hicolor/scalable/distributor-logo-Leap.svg, logo in GNOME Settings change to "Exclamation point". But no matter what icon I replace of there, it still doesn't appear. Or rather, it is there. If I switch to a dark theme, I see a small white dot instead of an icon. So, problem not in icons, that's for sure. I think, problem in gnome-control-center... but it is only hypothesis.