County Republicans said the ruling, issued in response to their lawsuit, is likely to end up affecting few ballots and would follow a process in place in Marion County under the previous clerk.
But it means that any ballots facing challenges won't be counted Tuesday or show up in election results that night.
Circuit Judge Theodore Sosin, a Republican, stressed after hearing four hours of arguments Friday that all valid ballots would eventually be counted.
At the center of the dispute are tens of thousands of early votes cast by mail or in person in an election drawing record interest.