As pstuart mentioned, one of the post mortem was to fix the script, which I did by using a temporary table.

The other part was to enable new columns to be added to that table in case we need in the future. For that part, I locked a few tables for writing, recreated them with a separate name and replaced the old with the new one in order to avoid any downtime or dealing with master-slave set-ups to be able to dump and restore without downtimes. Full vacuum freeze wouldn't reclaim that space back.

He used a temp table to stash IDs, like he should have from the start.