When you install the Modify ePub plugin, it adds a button to your toolbar. See first image below, last button on line 2. If you don't see this button, look for the 3 dots at the right edge of your main toolbar to expand the second line. Also make sure you've restarted Calibre after installing the plugin.
Once you've found the plugin button, go to the Calibre book list and select the ePub you just imported.
Click on Modify ePub. The second screenshot comes up. Check the box that you see I have checked. No need to select anything else. Click OK.
A job runs in the background and when it's finished, the message in the third screenshot pops up. Click Yes to replace the old EPUB file with the updated one. The original is saved as an ORIGINAL_EPUB file.
Email the updated epub file to your Kindle. If it looks o.k. you can delete the original_epub file.
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