Earlier today (11/9) I booked on aa.com an MSP-ORD-NRT trip, with the ORD-NRT segment being a JL codeshare. I have left a "full story" on the JL board, but what essentially happened is that AA assigned me seats on JL when I booked but never indicated that online (still does not, mostly). When I called JL, the JL agent told me I already had seats, which I had not known.
I then asked the JL agent to change those seats, which she cheerfully did for me by calling AA.