Modifying the archive works by re-writting the archive to include all files specified and then renaming the archive t the original name. When yu save the archive it is written to disk but the rename does not take place until the archive is closed. Thus to flush all changes to the original archive you should take the File/Close or File/Save,Close&Reopen menu options.
Newly added files are shown with a different icon symbol, and this will remain until the archive is closed (and re-opened).
Converting Formats
More is said about the supported formats in the 'Formats' section. However, you can convert between the supported formats simpley by using the File/Save As and using te extension that represents the required format.