Can't connect to Tekkit server, lagged out by floating blocks

I am running a Tekkit 3.1 Server on a Linux Debian 64 bit virtual machine with 4GB ram allocated for it. Today, I noticed a lot of lag, and then went to my quarry and noticed I didn't have my teleport pipe at the right frequency. Before I could pick up the blocks I was lagged out, and now I can't connect. When I try my client give me a gray screen. I stopped the server immediately to prevent more block from piling up, but I still can't connect.

How can I save my map? Is there a way to remove all broken floating blocks?