There are at least two issues going on here.
One of the failure modes has to do with the aging of the explosive agent, so it was decided to go ahead with the replacements, since they had fresh explosive material, knowing they would most likely, some would be replaced again, once the production records were fully obtained and production issues and changes were sorted out.
The other issue is hard FOD that turns into shrapnel. It was hoped that the problem was eliminated at some point in production and not all early replacement bags would be recalled. However Takata didn't just have poor production tracking, they had none. After defying a court order and being fined millions of dollars per day for not producing their production records, they finally admitted they had none.
In the end, nothing could be determined, so all the early replacement airbags are being recalled.