In calibre's Configuration directory.
Preferences ==> MIscellaneous ==> Open calibre configuration directory.
The default is %APPDATA%\calibre\ on Windows, or ~/.config/calibre/ on linux.
Bookmarks are saved in the file "iterator.pickle", but only for your user account.
They are also backed up inside the EPUB, unless you remove them, or set the option no to save them in the book.
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