How can I be positive that one of the incoming payments to my bitcoin-core was double-spent after it was confirmed once by the network, through the JSON-RPC interface?
Related questions:
If your node received the original spend, the listunspent RPC will display the transaction with "-1" confirmations, as will any other RPCs that would normally list the transaction. The source code calls this conflicted: "not in the mempool and not in the block chain." This feature was first included in 0.9.0.
If your node never received the original spend (perhaps because it was offline at the time) or the now-stale block that contained it, it doesn't have any way to know about that original spend, so there's no information you can get from an RPC.
listunspent doesn't return txs that have < 0 confirmations. listsinceblock will not show them either but you can use listtransactions instead which does.