Sounds like your best bet would be to remove the ballusters and install the floor. Then you can reinstall the ballusters on top of a plate, like a wall frame. The plate would be a 1x4 that you could attach to the floor with screws, or well placed nails. Make the plate to fit without nailing, then drill holes where the fasteners will go. Remove the plate and drill the holes in the floor out with a 3/4 to 1 inch spade bit. This will allow the floor to move a bit under the plate. Install the plate just snug, then cut and reinstall the ballusters. Leave the posts alone, just trim around them when the floor is finished. Be careful to nail the trim only to the posts.