"video showed regular ballot containers on wheels — not suitcases —" Nice nitpick.
The "refutation" of the AP is only someone saying "nah-huh" without evidence, as such it is a failed refutation.
"Other election workers started to pack up, Sterling told The Associated Press in an interview. They put prepared ballots back in boxes and away under a table “to close out for the night.” Members of the media and Republican observers began to leave the building too." So why did EVERYONE think that they where done for the night?
"The office said it had launched an investigation into why partisan poll observers left before scanning ended." So they don't know but made a statement of fact on the issue anyway.
"After a short period when observers weren’t present," So how many where scanned without ANY supervision? Let alone the basic amount. But the ballot watchers already left when everyone started packing up to quite for the night.
But it does support the basics of the claim being make as true while attempting to justify counting ballots without poll watchers present. And thus while trying to excuses the behavior, they confessed to it being done.