title_body: How do I prevent Calibre from modifying EPUB files when I read them?
upvoted_answer: I hadn't looked before so I did a little investigating. With Calibre 4.23 on Linux, I found that it's not exactly Calibre, it's the Reader.
  I don't know why this Reader (it's a newly re-written reader, but I don't know if the old one did this) is modifying the epub meta-data. There is no reason to do so that I'm aware of as bookmarks and other reading information is kept in the database.
  With that in mind, I changed the EPUB file permission to remove write permission. As a Read-Only file, everything seems to continue working normally and the Reader is no longer capable of changing it.
  So at this point I can only suggest:
  
  Change all the epubs to read-only
  Substitute a different reader
  Send feedback to Calibre
  
  additional info
  I did a little more investigation and found that &quot;ebook-viewer&quot; is writing meta-data under &quot;Miscellaneous&quot; &quot;calibre_bookmarks.txt&quot; even though bookmarks are controlled via the database. Deleting this entire entry via &quot;edit book&quot; has no effect and the book marks are still present because they are in the DB.
  The content written also includes: access time stamps, Book Title, and my User ID. It's written as JSON Base64.
  This should not be happening!
  I posted Bug #1894442
  Calibre Response
  Calibre says it's not a bug because most users prefer it this way. Nevertheless, it can be turned off by:
  
  LTrun {sic} it off under the miscellaneous section of the viewer
  preferences.
  
  
  Open the Calibre viewer
  Right-click the body of the book to bring up the controls
  Select Preferences
  Select Miscellaneous
  Uncheck &quot;Keep a copy of annotations/bookmarks in the e-book file, for easy sharing&quot;
  
  I verified that it worked (at least for one in a row).