I've set up a cobble generator with Buildcraft that will let flowing water touch flowing lava, push the cobblestone out of the way with pistons, retract, and allow another to be created and pushed out. I use a miner to get the block, but it pushes those pipes to the side that the miners make when digging down, and the machine stops when the piston can no longer push all the pipes.
I would have to remove them for it to continue, is there a way to delete or break those blocks?