When you are finished with a project you need simply to download the latest version of each chapter in the project, by using "Edit chapter" or "View chapter", which will open them in InDesign.
You can then save them in a new location (such as a folder on your desktop). When asked if you want to save the document as "CtrlPrint" or "InDesign" choose InDesign. The chapters can then be left locked by you or unlocked by clicking on the red padlock.
You will receive a warning if a file downloaded from CtrlPrint is opened in a version of InDesign without the CtrlPrint plugins - you can ignore this warning. To remove the warning export the document as an IDML.