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I see that. That isn't quite what the Wisc. Recount Manual says:

http://elections.wi.gov/sites/default/files/publication/65/recount_manual_11_2016_pdf_17034.pdf

It looks like board canvassers have great discretion about how to do the recount:

Unless a court orders otherwise, the board of canvassers may decide to either hand-count or use voting equipment to tabulate the ballots. The board of canvassers may also choose to hand-count certain wards, while using voting equipment to tabulate other wards. Wis. Stat. § 5.90(1).

If voting equipment is used, it should be programmed to read and tally only the results for the contest to be recounted. Prior to the recount, the filing officer should consult individually with board of canvass members to inquire how each prefers the ballots be tabulated. Based on that informal polling, the filing officer can prepare for the recount. The formal decision on the tabulation method to be used should be made publicly when the recount begins so as to provide an opportunity for candidates or their representatives to object.

plus the judges order isn't mentioned in Wis. Stat. 5.90(1), that I can find. (it might be somewhere else)

I'll be right back, I need to buy a whole lot more popcorn.