I originally booked EWR -> TXL in K-class and recently upgraded with points / cash to PZ class. I know that these fares earn miles based on the original fare class. Looking at my ticket now, however, it reflects "PZ" class and I am considering crediting to Avianca or another Star Alliance partner to get miles based on 50% of the distance flown rather than fare paid (just $150 each way).

How would I even go about crediting this flight? I'm concerned that Avianca will not see the original fare basis and issue no credits. I'm also Premier Silver and a credit card holder-- do I lose my normal benefits (free bag, etc.) if I input another frequent flyer number?