The visibility of categories that are specific to the link can be turned off in the Visibility/Graphic Overrides dialog, on the Model Categories tab. Any category that you do not want to show in the link but need to show in the host model must be handled differently. You will need to use the Revit Links tab in the Visibility/Graphic Overrides dialog.
The first thing I will say is check the simple things that you may think don’t need to be said, but I’ll say it anyways. Make sure you’re in the correct project, all the worksets that it could be on are open, and you’re in the correct view. Also make sure that a temporary view mode is not active. Sometimes we can get tripped up by the simple things.
In my experience, the primary aspects of your approach should include proper view ranges and turning off visibility with categories and filters. In other words, set the View Range for each plan view. Next, in the Visibility/Graphic Overrides dialog, turn off the visibility for the categories that should not appear. Then create filters to control the visibility of elements of the same category.
While we may be able to laugh at some of our visibility blunders, it can be a serious concern for organizations. As a BIM consultant, I have seen multiple individuals lose anywhere from 30 minutes to 2 hours a day struggling with visibility issues.