I'm so sorry to hear that you're having issues. My Surg always pulls all of the Fluid out when I get my fills. He will prefill the syringe with how much fluid he and I think should be added, finds my port, pulls all of the fluid out, flushes the line a few times, and finally puts all of the fluid in. Then we're done! I asked him last time why he did the put fluid in/ pull fluid out thing. He said it was to flush the line of any air pockets so that the fluid amount in there is a true amount.
But I've never had it hurt. It was uncomfortable when he was doing it but not bad.