ZipGenius allows to rename an archive without quitting from the program.
Click on "Rename Archive" in the "File" menu or in the sidebar to do that. Also you might click on "Archive Properties" to see a dialog reporting info about current archive: here you can type the new name you want to assign to that archive and click on "Rename archive" button to complete this action.
WARNING: nested zip files can't be renamed if it is open in ZipGenius, but you can do that when you see that archive in the file list related to the main archive. You have to select that zip as you would do with other files, then click on "Rename file" in ZipGenius popup menu.
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