They have often indeed made “flight spare” copies of the main instruments.

When I worked for Mars Global Surveyor, one of the museum-pieces in the lobby was a glass case with the Viking spectrometer flight spare.

The flight spares were exceedingly useful when the spacecraft had some kind of trouble during its mission, because you could mock-up the flight spare in a lab and replicate many situations very closely, and propose solutions based on the mockups.