sorry, when I put the file on the AppData folder, it did stay on dark mode, but the red boxes issue wasn't fixed (even after commenting the stuff out)
in Geany, press "tools" > Configuration Files > geany.css
Ctrl + F ": image(-gtk-recolor(url("assets/scalable/small-checkbox-unchecked-symbolic.svg")), -gtk-recolor(url("assets/scalable/small-checkbox-unchecked-symbolic.symbolic.png")));" put #/ at the beginning. Put /# at the end. Ctrl + S Close, reopen. Checkboxes work now.