Don't append the preferences, trash them. Quit Quark, find the preferences file (In Mac OS it is HD>Users>Your_User_Name>Library>Preferences>Quark…for Windows, please search the forum) and move the folder to the desktop. When you start Quark again, the program will see that the preferences file is not where it is supposed to be and create new preferences in the correct location. If the problem persists, it was not because of bad preferences. At this point, you may leave the preferences as they are, or replace the new preferences folder with the old one (do this while Quark is not running). If you would like to keep the new preferences, you won't need the old ones, so you may move them to the trash.
Append is a method to transfer data from one document/project/Quarkfile to another. It is a file-to-file process, not a page-to-page process. You start by creating a new Quark projet that has the same size as the one you are having trouble with. Because you can have more than one layout inside a project, you can append (or add) a layout to an existing project by gathering it from an existing Quark project file. You do this by taking the new project file and go to File>Append and navigate to the Quark file that is giving you the problem (it should not be open). Inside the Append window, there are several types of data that you can copy from the old project file to the new one, including layouts (the actual pages of the document). While you are in the Append window, you will probably want to also copy the colors, stylesheets, lists, or anything else that you created in your old project that you don't want to have to create again.
Appending data from the old document may allow you to copy the good parts and leave behind the bugs that are causing errors, but maybe it won't help. Sometimes files are broken and can't be fixed. You may have to start over and create it again.