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Here's the digestibility study: https://sci-hub.ru/10.1007/s13197-020-04249-0
First, this is an in vitro study. No actual tests on living organisms. This isn't unusual for an initial study and it's easier to get it approved. The procedure was simple, they mixed gluten flour with water, and compared the differences of leaving it as is, traditional stewing and microwaving it at different powers and times. What they found was that at the higher powers (1000w for 5 min) there was increased cross-linking of some amino acids. This makes it harder for them to be absorbed, notably Cysteine was decreased after microwaving. This decrease only significantly occurred at the higher powers and time of microwaving. Digestibility decreased about 9% from stewing to microwaving at 200w for 1 minutes(52% to 43%), but the difference from 1 minute to 5 minutes at 200w was less than 1%. There was a decrease to 40% for 1 minute at 1000w and a further decrease to 34% digestibility for 5 minutes at 1000w. However, the paper also notes that gluten flour already has poor digestibility(52%) compared to regular wheat flour (77%), soybeans (78%), and bread(97%). Also noteworthy is that stewing decreased digestibility from 52% to 47%. They also measured several products of a specific chemical reaction called the Maillard Reaction. This reaction is what causes meat, bread, and vegetables to brown when cooked. The 3 products they measured were 5-HMF, Fructosamine, and Melanoidin. All of these were increased with microwaving at any level, but not being notably increased with the lower microwave settings (200w). In terms of health effects from these, nobody is really sure. There just isn't a lot of research on them.
So this really doesn't contradict the previous study. Just microwave at low power and low time. Or better yet, eat something other than gluten flour if you're that concerned.