And yet it seems that it was flagged as one, according to the agent you spoke to. Is there any other information you can share that might help us figure out what happened here?

The dupe detector flags and cancels many things it shouldn't.

And I held multiple conflicting bookings for many years, sometimes ones that actually violated the tariff (multiple reservations on the same O/D pairing on the same date), and never once had a problem, until Amadeus. Any experiences that pre-date Amadeus's introduction really are no longer applicable. It's possible AC has it set up to try to catch nested bookings, since in some cases these might constitute back-to-back ticketing ("the combination of two or more round-trip fares end to end for the purpose of circumventing minimum stay requirements", per the AC tariff), which is prohibited by the tariff. On a domestic trip where everything is priced as one-way, that's clearly not applicable, but we've already proven that the dupe detector is frigging stupid and cancels things that (a) don't violate the tariff and (b) aren't even necessarily illogical.