First, it wasn't a good ideal to keep bearded dragons of such difference in size together. Second, I don't think the larger one would have eaten the smaller one, but it is possible (especialy if the larger one looks really stuffed). Most likely the smaller one either buried itself under something (if substrate sand, may be underneath it, or paper towels etc) or managed to leap out trying to save it's life.
Search the cage completely, sift through sand, lift papertowels or newspaper, check under all furnatures. If not found, check around the cage, in dark narrow corners. Oh, if you have cats, it is possible the cat may have jumped into the cage and got him.
When you find the other dragon, put him into his own properly set up cage. They will do much better alone than together.
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PHLdyPayne