Depending on the location and the depth of the scratch, yes and
no.
Take your stone to a local jeweler and ask for advice about
polishing out the scratch. If it's superficial and shallow, the
jeweler may be able to polish out the scratch.
If, however, the scratch is visible and deep, the stone may have
to be re-cut in order to give it a value, and the new value of the
smaller stone may be less than its original value.