I've been accumulating a mental list of properties that would support less-exploitable, more-auditable paper balloting. This has a surprising number of the properties.
The main items I don't see represented are all roughly related to auditability for ballot chain of custody. I think issues/irregularities with the ballot chain of custody are probably good proxies for triaging hand-audit efforts.
The goal is knowing when ballots go missing, or turn up in unexpected places (but I'm not sure where the sweet spot is for securing that chain without making individual votes unmaskable). I think it's a similar process, with lots of identifiers, and lots of scanning. It would live or die by rapid, simple, reliable scanning.
This means scanning identified ballots into shipping boxes, and generating an identifier for the box based on which ballots were scanned in. A pallet gets an identifier based on the boxes that went in. Shipments get identifiers based on whatever combination of boxes/pallets they contain. Scan in boxes at the polling station and accumulate identifiers for the polling place. Perhaps per poll worker. Scan ballots out of the boxes, back into the completed-ballot boxes and/or trash. Cumulative identifiers for completed-ballot boxes, trashed ballots, and unused ballots are scanned back out of the poling place and at each step back up the chain again.