My answer would be that the AP is just reporting the claims made by the two parties, rather than knowing that they were destroyed - that's the usual approach from the AP. I agree there's likely no "smoldering trail" in any logs that an encrypted system like Signal might be able to furnish, but I also am not read up on what kind of reporting requirements they might have. If they have to do something like SMS carriers where "a message was sent at x time on y date" logs exist then there's investigatory potential. But again, not really my strong suit.

There's probably some testimony or interview that we're not privy to that lends credence to these claims by the FTC, hopefully it will be made public as their efforts progress.

Moreover, do we know the conversations were destroyed AFTER they were ordered to preserve them and not just routinely destroyed?

Can't say. My own anticapitalist leanings notwithstanding, none of the reporting on Amazon's corporate behaviors would lead me to believe that they are pro-consumer or unwilling to break the law in furtherance of avoiding a heftier punishment.