I did it by phone or agent (tst office). Works perfectly. Example. Flew jfk yvr hkg. Check in at
jfk. Both boarding passes are printed. Aa emerald on yvr hkg and Alaska number on jfk yvr.
(Jfk yvr in I class and yvr hkg in r class - I am both Alaska and aa top elite)
I put different number for every segments for my 14 sectors tickets and the boarding pass printed correctly (only ay codeahare on qr and aa has problem posting)