The amount of applicable lines involving the scratched runner will be refunded, while the remainder of the bet will still stand.
For example, in the bet below, if number #3 was scratched, the applicable combos involving the scratched runner would be voided (1 combo at $2.50) and the remaining bet will stand. The new bet will then be #1 win and #2 to come second.
As another example, in the bet below, if #2 was scratched, the applicable lines/combos involving the runner will be voided/returned. In this case, as #2 needs to run 1st or 2nd for this bet to win, all combos are void and the $5 stake will be refunded.