When cutting through a section view (or sometimes elevation views), the topo from the linked file disappeared.
However, the topo showed perfectly fine in other views
I checked all the possible causes like VG (Visibility Graphic) setting, workset or even element hide. Nothing seems to be the culprit of this issue. I ended up stumbling a very subtle setting that caused this issue. It had to do with the Far Clipping setting from the view properties. Turns out if the Far Clipping was to set to "Clip with line", the linked file would disappear.
If you are not sure what this setting does to your view, Autodesk Help page (see below) has a good image to show the differences between these "Far Clipping" settings: