This has happened to me occassionally also. The specific circumstances vary, but often results from a change in an international flite operated by another carrier. Alternatively it could indeed be the application of a SWU to an AA flite.
This situation is intentional and not some type of unplanned glitch. Usually the changes are not material, but maybe not. So it is best to call. A reservations desk, rather than CS or AAdvantage is more likely to have agents who see this issue more often.
For me the itinerary sometimes does not reappear automatically, so ask to have it replaced on your my reservations.
Rens