If you have created a project with more than one TOC you will also want to choose the TOC you want to use in your output when you publish. You can select this directly in the Publish dialog:
When you select an additional TOC to publish with, all the topics in that TOC will be included. In addition to this, topic files linked to in the TOC may also be included in HTML-based output formats, depending on your settings. See Multiple TOCs for more details on managing this.
You can select your additional TOCs in the Publishing Task Manager in the same way as you do when you are publishing manually.
Command line publishing
You can specify additional TOCs in your command line directly with the /TOC= switch.