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Well, I finally found the answer to my question. The fish suffocate to death. When a whale swallows fish whole, the fish go into a non-enzyme secreting stomach. Here, anaerobic bacteria slowly break down the fish into a soup, which passes through a small opening into the other stomachs.
Anchovys in a Bryde's whale stomach
Salmon in a minke whale's stomach
From the pictures, it looks like the stomach may not move much. The fish appear to be intact.