I believe a lot of the ballots that have been disputed were mail-in ballots.
Mail-in ballots, in Texas, and I think in Minnesota, have an outside "carrier" envelope, then an inside envelope. The carrier envelope has the signature of the voter, and whatever else information the law requires. On election day, the carrier envelopes that are deemed to be valid are opened, and the interior envelopes, which have no markings, are mixed together, then opened and counted, which preserves the confidentially of the vote. The carrier envelopes which are rejected are not opened, so you don't know who the voter voted for.
Per previous posts by Powerline, Franken's campaign did a great job, and Coleman's campaign did a pi@@ poor job, of contacting the voters whose carrier envelopes were deemed to have not complied with the law, and whose votes were never counted. Everyone who told Franken that they voted for him was noted by the Franken campaign, and the Franken campaign immediately went to bat to get those votes accepted and counted in the recount. Coleman, by and large, did not do that, so he did not know which carrier envelopes to try and get counted during the recount process.
Thus, since Franken has already cherry picked the carrier envelopes for "his" voters, the balance of them should favor Coleman.
Does that mean that Coleman can convince the Court that the carrier envelopes were improperly rejected, and get them opened? Who knows. It does appear to mean that he will have a shot at it, and his hopes, while still dimly flickering, are brighter than they were.
Does the election commission of each county notify the people that their ballots were rejected?
But I would bet that Coleman picks up MUCH more votes when the counties are ordered to use the same standard when counting.