Yes, you do. The important point here is that there are two different companies. They are NOT one company.

Original airline will manually give you miles because they screwed up. You have to ask, but they do it for customer service since you bought a ticket with them, and they could not follow through. Does not matter if you took a bus, train, taxi, another airline or rental car. Bottom line, they screwed up (or had some problem)

The new airline is carrying you as a paid passenger. They really do not care WHO paid for the ticket, just that you flew with them. Therefore, they will give you credit for the flight as always.