Flurry of Blows explicitly makes two unarmed strikes. So if you are asking if the attacks are with the bigger weapon, the answer is no. If you're asking if you can do in unarmed while holding a bigger weapon, the answer is yes but it's not what you may be expecting. Under Martial Arts you only get a bonus to unarmed damage when unarmed or wielding Monk weapons, and that's also what would allow you to use Dex. So yes you can make a flurry, but it would be with two (1 damage, uses Str only) unarmed attacks. Unarmed Strike is listed under weapons the equipment chapter.
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