The "Double dipping" term is a stretch. After all, you only get credit once on each airline.

Airline A had a problem. You paid to fly on them and they reward you with miles. The fact that they have to get you there via another method is a different issue.

Airline B now gets your business. They reward you for your flight. They don't seem to mind how you wound up their flight, just that you are there.

Some airlines will handle the lost segment/miles on the first airline on the spot. Delta agents used to send an email or something to Atlanta and they posted it right away.