Well, you can always tape it off, that's option 1.
If that won't work because of where the scratch is in relationship to the design, you can paint on a bit of emulsion on both sides, being careful to both emulate the same thickness as the rest of the screen (not too thick, not too thin so as to be useless), and to not get it in your open areas of the design. Then re-expose and washout. that works too. You just likely need a small brush or q-tip.
Touch up is part of the preproduction step, during makeready. If it is only a pinhole or crack - or even a big one - you touch it up. Water resistant for waterbase, water soluable for solvent base. or emulsion. Whatever, put it on smooth, thin, and on the bottom of the screen. Small brush and small chunk of squeegee for spreading larger areas.
And tape works fine, except when it doesn't.
If the emulsion is in the wrong place - you have to take emulsion off.....in that case, you would probably redo the screen. Although you can work with stencil remover on a q-tip in certain cases.