As far as I know, reservations can't be combined once they are split.

In the future, if a flight comes up as "direct", use the multicity option to split up the flight. If the direct flight is LAX-BOS, with a stop in MSP, search LAX-MSP-BOS and the segments will ticket separately. If a schedule change results in a direct flight, you may end up with one or two segments for the "direct" flight. YMMV.