Referenced Topics and Popups are read-only when viewed within a master project. To make changes to them they need to be edited within their original project. You can either do this directly by opening the project using "File | Open Project", or you can go to the Properties tab of the referenced page in the master project, and click on the [Edit the Original] button.
This will load that page in the original project. Once you have made any changes, you can click the [Refresh from Original] button to reflect the changes.
If a referenced page has been deleted from the slave project, the next time you load your master project, the icon in the contents tree will have an "X" overlayed on it to show that it is missing, presumed deleted.