Once you have imported and integrated the web pages under a topic root directory, you can safely delete the backup files (files with .bak as name extension). You can also delete the shortcut files but I recommend that you keep at least the first shortcut file that started your topic root (usually the home page of a web site). You may view then remove the ShortcutList.lst and the REPORT.txt files. I personally keep them.
You can move the whole topic root directory into another directory of your system, without affecting the imported web page display nor the hyperlinks.