You can select individual faces in edit mode and delete them by pressing "X", then select "delete faces".
For this scenario you could also (with that face already selected)press "G" to grab and "Y" to lock it to the Y axis, then enable snap to faces and hover your mouse over the face that's black in the picture(it's normals appear to be inverted but that was not the question). .
Move, along an axis and Snap To enabled, the opposite face that's inside. If the handle is sheared snap edges as well. Having done that you may remove the unnecessary face to save resources.
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