I think it would have to be a fresh vote across the state, if that is what the court orders, not just those two electorates, mainly because it would be conducted as a fresh by-election. New candidates could nominate, or old ones drop out, so it would be impossible to align the new results with the old. The elected Senators would also likely be up for re-election, too, due to the quotas required. If those final two spots were the only ones declared open, the quota would be a third of the vote, not the one-seventh the others received, and would almost certainly result in one Liberal and one Labor Senator being elected.
Is this true? If you seat the folks already duly elected, you can count them as three full, and one full quota respectively. The Liberals could win one of the remaining two seats by taking 64%, or so, of the vote. Otherwise, they would fall short. Labor could conceivably win a second seat.
What is to stop folks from arguing that it is the composition of the Senate that has not been decided? Sure, the source of doubt is WA, but, then, again, the source of doubt is in only two of the seats in WA. What's the difference that makes a distinction between having the doubt localized to one state, or two specific seats within one state? What we know for certain is every declared winner in the Senate but two were in fact duly elected. Why not rerun the entire Senate? Presumably, the rules call for the simultaneous election of half the Senate.
What is being argued here is an alleged lesser of two evils that is nevertheless quite evil. The precedent would be horrible: if you don't like the results of the election disappear some key ballots to force a new election. There has to be a better way than failing to seat duly elected members. How about invalidating the second count, and commencing a third count with the results from the missing precincts from the first count being presumed accurate? Or, a referendum, PUP/Labor or SE/GREEN take your pick? Or an election between those four candidates for two seats? Or, drawing straws between Shooters and Christians? Or, drawing straws between PUP/SE and LAB/GRN?