For the second time in two days, a former Minnesota Pollution Control Agency (MPCA) official defended her decision to delete e-mails related to concerns over the agency’s handling of PolyMet Mining Corp.’s water-quality permit.

The complicated permit, running hundreds of pages, was a major triumph for Toronto-based PolyMet when the MPCA finally issued it in December 2018. The permit has since been suspended, and construction of the copper-nickel mine in northeastern Minnesota has been delayed amid accusations that the MPCA and U.S. Environmental Protection Agency conspired to hide the EPA’s serious criticisms of the permit, meant to control pollution from the controversial mine.

On Friday, on the fourth day of a trial-like hearing in St. Paul into whether the agency bent the rules as it drafted the permit, former MPCA Assistant Commissioner Shannon Lotthammer was back on the stand in Ramsey County District Court before Chief Judge John Guthmann.

John Martin, an attorney representing the MPCA, argued that neither Lotthammer nor the agency tried to suppress anything related to the permit and had sought ample public input on the draft.

He painted a picture of an agency struggling to make the required responses to the hundreds of public comments to the draft permit when it was opened to public comment last year.

As she did Thursday, Lott­hammer testified that her e-mail to the EPA simply asked the agency to hold off submitting its formal written comments on the public draft of PolyMet’s permit until after the public comment period closed, and to wait so that the MPCA could give the EPA a new draft that incorporated public input. The EPA would then have 45 days to respond.

The approach “just made a lot of sense to me,” Lotthammer said.

She defended deleting the e-mail, saying it followed her understanding of the MPCA’s rules on record retention.

She also clarified that the new term “pre proposal permit” — a new designation for the draft the MPCA finally gave the EPA after altering the public draft in response to public comments — originated with the EPA but wasn’t necessarily created by Kurt Thiede, the EPA official she was negotiating with. Thiede is now head of the EPA Region 5 office in Chicago, which oversees Minnesota’s enforcement of federal water law.

“Did you ever try to hide the fact that you had made this request to EPA?” Martin asked Lotthammer.

“No,” Lotthammer said.

Lotthammer said she did not know about the phone call that was made after the public comment period was closed, in which an EPA regulator read the EPA’s lengthy criticisms of PolyMet’s water permit over the phone to MPCA staff.

William Pentelovitch, an attorney for a coalition of opponents — environmental groups and the Fond du Lac Band of Lake Superior Chippewa — painted a very different picture.

The MPCA was not focused on efficiency, he implied with his questions, but rather, was trying to keep the EPA’s serious criticisms of the permit out of the public eye. The permit regulates pollutants, such as sulfate and toxic heavy metals like mercury and lead, that a facility can discharge in wastewater flowing into the environment.

He showed various MPCA documents outlining which records and e-mails and memo employees must preserve or can discard or delete, and argued that the e-mail Lotthammer sent to Thiede was clearly agency business that required preservation.

Lotthammer disagreed, calling the e-mails “developmental materials” that didn’t need to be kept because they weren’t final actions.

Pentelovitch also produced the public statement the MPCA issued early last year about accusations of suppression when they first surfaced, a statement the agency sent to the governor’s office and to lawmakers in the state’s Iron Range delegation. It said: “The MPCA did not, at any time, ask EPA to suppress or withhold comments on the PolyMet NPDES permit.”

Lotthammer said she stands by her testimony.

“We did not ask them to suppress or withhold statements on the permit,” she said. “We did ask them to consider holding off on comments on the public notice draft of the permit.”

When Pentelovitch asked Lotthammer if the MPCA’s official public statement misled lawmakers and the public, she said no.

The MPCA was trying to explain the process “succinctly,” she said.

The evidentiary hearing continues Monday and will likely last all next week.

The allegations of “procedural irregularities” in the permitting are just one of several challenges PolyMet faces. Two other investigations into the permitting issue also are underway: one by the EPA Office of Inspector General and one by the state Office of the Legislative Auditor.

The mining company must also contend with two lawsuits in U.S. District Court in Minnesota — one filed by the Fond du Lac Band and the other by environmental groups — asserting that the permits issued to PolyMet violate federal laws, including the Clean Water Act.

The Minnesota Court of Appeals also recently kicked three other PolyMet permits, all issued by the state Department of Natural Resources, back to that agency for further consideration.