Here is how to set Calibre to not update the metadata when Saving to disk, using the viewer, and using the editor
Saving books to disk
Preferences > Saving books to disk
Uncheck Update metadata in saved copies
Viewer
Preferences > Miscellaneous
Uncheck Keep a copy of annotations/bookmarks in the e-book file , for easy sharing
Editor (this only works for ePub)
Load an ePub in the editor
Edit > Preferences > Integration with calibre
Uncheck metadata in the book when opening
Exit the editor without saving the eBook.
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