Program settings (including bookmarks, history, etc.) are usually stored in real user home profile folder or registry hive. For the isolated program to use them, they're copied to the isolated environment. This way these settings persist between reboots, if you start the program in isolation. But this program being executed unisolated will use old settings from real user. This was done this way for security purposes. Otherwise if for example some exploit for settings is possible, malware having infected the isolated environment could spread to the real user via infected settings.