In order to save emails in the PDF file format, select File ▸ Print and then choose Print to File. See for general information on printing.
You can also export messages as PDF by dragging and dropping them to the file manager, instead of dropping them in mbox (text) format by default.
Open the Terminal application.
Run the command gsettings set org.gnome.evolution.mail drag-and-drop-save-file-format 'pdf'
You can also use the dconf-editor application to do this.
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