I think that gets into a slippery slope since flagella are generally less useful as the mass of an organism goes up, which is why they generally disappear after a certain size and then larger morphology takes over (think of using only your fingers to swim). But it can easily be made so that this size-scaling only goes up to a certain size.
Atleast flagella are easy to tinker with (I think?), so we can easily alter them and try another thing soon after if the first option doesn’t work.