When you select the Id for the file to delete in the last step, it needs to be from the original Create file step in the Flow (which creates the .eml file) NOT the Create file 2 step (which creates the .pdf file). When you create the Delete file step, the dynamic content starts with Create file 2 since that was the most recent step:
List of dynamic content from Create file 2 step
But if you scroll down further, you should be able to select the file ID from the original Create file step and delete that file instead.
Dynamic content from the original Create file step