ABS pump replace, does bleeding the brake lines get rid of air that might be in the abs pump?

Hello, I just replace the abs pump on a 06 Prius but I am going to take the car to the dealer to get the brake lines flush/bleed since I was told you need a special tool to bleed the brakes. Would like to know if by bleeding the brakes would that get out any air that might have gotten inside the abs pump? Was told by the dealer that will only flush the air out the brake line system not the abs pump, but isn't that part of the braking system all connected together?

 

Yes, They charge me $200 to fix it. I thought the bill was going to be over $600 because the car was at the dealer over 4 days. They thought I had an electrical problem, the mechanic had taken the front dash apart to look for a short somewhere on the wires because they were getting alot of code on the diagnostic, when they check those parts everything was OK. The guy even took the car home with him to see how its running. But I had told them at the beginning when I drop the car off that I had rebuilt the car & had to replace the abs pump & the abs pump relays for it, but the guy never told that to the mechanic. I went there & told the mechanic what I had done & thats when he figured it out since he was never told the message I left.