PNR is still in use. I can reconnect once it’s used up to see if there is still a discrepancy. Is your thinking that the difference may be reconciled once the last flights are taken? Like TK shorted but LH might make up the slack? I just wasn’t sure how the tool divided it up by segment.
SQD is always pro-rated based on distance.
SQD per flight = total itinerary SQD / flight's share of ticket distance.
If it were a dollar or two, it's possible it's just rounding and would get made up on later flights on the ticket, but with the size of this discrepancy, it's much more likely you'll end up writing in to get it corrected. You don't have to cite the cowtool when you write in; when you point out that it's wrong, they'll go look at it and correct it.