Topics and their TOC entries are two different things. The topic content is actually stored in the topic file, which is stored in the Project Files section of the Explorer. The TOC entry is really just a hyperlink to the topic file, which is stored in the Table of Contents section of the Explorer.
When you click on a TOC entry, the topic file is displayed in the editor for editing, but this is just for convenience. there are not actually any topic files in the TOC, when you click on a TOC entry and edit the topic you are actually editing the file stored in the Topic Files section.