Experienced a similar issue with AA and Qatar in 2023. Short answer was that the duffel bag was transferred from AA to Qatar but the gun case needed to be picked up and checked-in at the Qatar counter.
Jennifer at Travel Express told me that is what I would need to do, but upon landing in Philly (outbound leg of the flights) for my transfer, the crew at Qatar called my cell phone and told me that they had my bag and to proceed directly to their counter for the firearms formalities. How they could have "had my bag" was a bit of a mystery because they called just after the AA flight landed and we were still on the apron taxiing towards the gate, but... I proceeded to the international terminal where they again informed me that they "had my bag" but that I was not allowed to travel with firearm and ammunition in the same bag. OK, but the rifles were not in the duffel, they are in a separate gun case. That's when they figured out that AA had checked the duffel through to Windhoek but the gun case only to Philadelphia. Because of this, the gun case wasn't showing on their system. One of the QA agents and I made a bit of a mad scramble across the airport, retrieved the gun case, and the rest went smoothly from there.
Seems like more of an ongoing communication issue than a new policy. At least, from where I sit.