)Possible loss of miles for dropping segment
 

Without going into all the details, I am planning to go CDG-AMS-JNB-AMS on a ticket that is routed CDG-AMS-JNB-AMS-CDG. If I stay in Ams and just let the final Ams-CDG segment drop is there any chance that for some reason I won't get the miles? If it matters, I will be flying the day after my arrival Ams-B0s-Ams on another ticket and don't want to have to go all the way back to Paris and then come back. The alternative is simply booking Ams-JNB-Ams and taking the train Paris-Ams on the way out.

Thanks for any suggestions/advice

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Why would you expect to receive miles for an unflown segment?

It is of course not the 500 between Ams and CDG I am worried about but the 11,000 between Ams and JNB. Technically, I haven't flown the ticket I booked. If I had let the first segment drop, they would have cancelled the whole ticket and made me buy a new one. They can't do that if I drop the last segment but my concern is that it will effect the miles on the flights I actually took.

Oh no, I wouldn't worry about that at all.