In 2002, researchers for another project — the replacement of the Alaskan Way viaduct — drilled down into the ground to take water samples.
The tunnel that Bertha's digging isn't another project — the whole reason for digging the tunnel is to replace the Alaskan Way Viaduct. See here.
The wells were drilled in 2002 to study the ground after the 2001 Nisqually quake. But that's a related project, because the Nisqually quake is the reason why we got to thinking about a replacement for the Alaskan Way Viaduct.
Am I making sense? I hope I'm making sense. At any rate, the story summary needs updating.