yeah you can sand them down with some 600 and once youve got the run out you can sand out your 600 scratches with some 1000 and then re base it and you should be fine
you can sand them down and then rebase no problem. you can either use a scuff pad or 600 grit paper. you may want to wet sand it. base clogs paper quickly. good luck.
^^hes probly talking about clear coat ive done that afew times for clear and it works great as long as your carefull but on base coat you will want to wet sand with 600 then 1000 like said abouve
let the base flash real good,you can rake some 600 grit paper in one direction, sometimes this prevents the paper fom clogging so much. sand the run flat and base away...good luck