The Changed Files tab contains the list of files you or GNTool have modified in the uncompressed directory. These files will be recompressed and moved upon building an ISO from the File menu. You can also right click on any changed files in the Changed Files view to open them, open their directory, or revert the changes.
The Missing Files tab contains the list of files that have been removed from the uncompressed directory. You will only be allowed to build with missing files if you allow GNTool to create 1 KB empty files as a replacement for them.