Symbiosis in Cell Evolution (Margulis, 1981) includes the proposition that endosymbiotic spirochaetes became eukaryotic flagellum and cilia, though it hasn't gained much favour since both structures lack both DNA and ultrastructural similarities to bacteria and archaea.
MM, it wouldn't have happened with the prokaryotic flagellum. I don't know of any prokaryotes that have been the larger beneficiary of endosymbiosis. Also, the bacterial flagellum is a molecular engine with rotary parts, it would be like expecting an outboard motor to sail without a boat. And the bacterial flagellum is already understood to simply be a Type III secretory and transport system (normally used to injected eukaryotic cells with toxins) with a long and large protein chain on the end of it.
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