But were the making the changes properly? You are lucky that none of your segments on other airlines got "accidentally" cancelled when you made the changes with AA RTW desk (sometimes it happens if they forget to input the ticket number and associate it with the segment as some carriers would cancel segments if no ticket number is received after a certain deadline).

When changing a flight, the AA RTW desk needs to make sure that each new segment booked must be associated with its own SSR TKNE message line that is sent to the other carrier (linking the new segment to the 001XXXXXXXXXX ticket number).

FYI, As far as I know (from a Sabre TA's point of view), when flights on CX are rebooked (no change in routing, but change of flight/date) and CX 160 e-ticket stock is used, the e-ticket record automatically gets updated if cancellation of the old segment and rebooking of the new segment is done in the same transaction. Otherwise, a SSR TKNM 160XXXXXXXXXX message (manual ticket number entry) will have to be associated to that "new segment" and and OSI CX ET message sent as well so that CX would re-link the segment to the e-ticket (as the travel agent version of Sabre does not allow agents to enter the SSR TKNE message which automatically links the segment with the exact e-ticket coupon directly [to prevent fraud?]).