Here's another similar question about "combining" reservations (but somewhat embarrassing, as I am not an FT or UA newbie): Is there a way to link a paid and an award res, at least if the carriers are the same or in the same alliance?

Sometimes one finds a cheap fare from X to Y (a long distance, maybe even international trip), but adding Z (which might be only a few hundred miles beyond Y) adds many hundreds of dollars to the fare. So one books the paid ticket from X to Y, and redeems miles for the short hop from Y to Z (or maybe Y to Z is even a "long hop," but still relatively overpriced for the EQMs you earn!).

I've done this type of thing a few times, and never ran into misconnect problems as the flights were all reasonably on time, but am concerned what would happen in the case of irregular ops. Will annotating both reservations at least be helpful in such an event?

Let's hear from the experts on this forum, especially the "flaky" ones (you know who you are! ).