[KevinH]

Try Sigil's Restructure Epub to Sigil Norm tool.

The Custom design tool is to create a custom folder structure for a new EMPTY epub, not to restructure an existing one. With this tool you can create any folder structure you like and then drag and drop file type markers into folders to say where files of specific types should be stored. Again, only to design an empty epub to be filled in later.

My guess is Calibre has its own restructure tool. FWIW, The biggest things causing long loading times for most epubs are when people do not split chapters into separate files, mistakenly trying to keep all of the text in one file. Both Calibre and Sigil have tools to help properly split files into chapters.

You can also use Sigil's BookBrowser right-click pop-up menu to move files between folders while maintaining links. I am sure Calibre has something similar.