What to do, what to do. My thinking is always to emphasize getting fit over getting a bike fit. Obviously riding will increase fitness, sort of the whole point, but how to get from here to there? My advice is to ride the 54 with the new fit, ignore what it looks like. What it looks like or what other people think doesn't matter. Just find a way to ride the bike and do it. The bike shop and fitter are both right.
The real issue is how to progress and get fit. The bike is just a tool toward that end. The usual method is to measure your weekly mileage using a bike computer and putting your numbers in a spreadsheet or just writing them down. Increase weekly mileage by 10% for a few weeks and then cut that back to 5% a week. But don't think you can ride the weight off. That doesn't work. You have to reduce your daily calories. I know, bad news, but that's how it is. The bike will help some. It will gradually improve your musculature and more muscle burns more calories, so that's good.
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Results matter