The scenario where D4.5 would apply:

You plan to have 3 round robins in stage 3 of your regatta. You complete 2 round robins and 50% of the third. Therefore the third round robin will not be scored (D4.2b)  

So when you get to D4.4(a) and look for the highest number of races wins, you would include the race in the third round robin for D4.4(a, b, c).

You would not include incomplete races from an incomplete round robin in stage 2, due to the limitation at the start of D4.4 'only results in the stage' as the incomplete round robin is part of this stage:

I think the team sailing umpires manual makes it clearer (http://www.sailing.org/tools/documents/TeamRacingUmpireManualJune2018-[24091].pdf section 13.7):

 

I think Ross has a good question.  The scenario is this:  Stage 1 is scheduled to be two round-robins of the entire set of teams at the event.  One round is completed the first day, and the second gets in about half the races scheduled.  The next day dawns calm and the organizers worry about getting in the entire format, so they terminate the round in progress and proceed with Stage 2, which consists of Gold and Silver leagues based on the results of the completed  round.  There's a tie between teams A and B for the position determining entry into the Gold league, but fortunately they met in the incomplete round and A wins the tie.  In Stage 2, three rounds of each league are scheduled.  The race committee completes two and a half rounds in light air before the wind finally dies out for good.  Teams A and C are tied in the Gold league.  As it happens, they raced against each other in the terminated incomplete round of Stage 1 but not in the terminated incomplete round of Stage 2.  Ross's question is, should the race in Stage 1 be used to break the tie? 

It's pretty clear to me that the answer is intended to be "no", as implied by the title of rule 4.5 and by the words in D4.4, "using ... only results in the stage."  Why would one method of breaking ties be restricted to only races in that stage, but not the other?  But titles are not rules, and D4.4 is not D4.5, so Ross is right, there's an ambiguity.   

I'll propose to the TR Rules Working Party that we add "in that stage" to the end of the first sentence of rule D4.5.  It would then read, " Ties in an incomplete round-robin stage shall be broken whenever possible using the results from races between the tied teams in any incomplete round-robin in that stage."

By the way, there's some skill required in designating stages of an event, and those stages should be laid out clearly in the SIs.  Clearly, no stage should contain both round robins and knockouts, as then the rules simply don't work.  Ditto any round robins with different leagues of teams.  In particular, if we use one set of rounds  to decide leagues for the next set (as in the story above), the qualifying rounds and the next set of rounds should be in different stages.  Also, if scores are to be brought forward from one stage to the next (as is generally done in the US), some provision has to be made in the SIs about how to handle completed rounds scored using percentage of wins per D4.3(b), because you can't add percentages.  I suggest that, if percentages have to be used in an early stage, teams' race wins be calculated as 

          (race wins in the stage) = (percentage of wins in that stage)*(number of races originally scheduled for each team in the completed rounds of that stage)

So, in the story above, if all teams did not race the same number of races in Stage 1, each team's race wins would be calculated as (percentage of wins in Stage 1)*2N, where N is the number of teams in the event.  Then those race wins can be brought forward to the next round.

D4.5 could be made clearer to make it obvious that it is not a way to score the incomplete round robin. The start of it is 'Ties in an incomplete round-robin shall be broken whenever possible…' making it sound as though it is possible to score an incomplete round robin (eg less than 80%).

Maybe something along these lines:

Ties in a stage with more than one round-robin shall be broken whenever possible using the results from races between the tied teams in any incomplete round robin in that stage. Other ties....

The other thing that D4.5 leaves open is how to handle a three way tie if all three races hadn't been raced in the incomplete round robin. (Eg Teams A, B and C, A & B and A & C have raced but C & B haven't raced). 
 
I think the scoring for anything other round-robin and knockouts should be left out of the rule book. We could end up doubling the size of the rule book if we had to codify everything that happens in the swiss league. 

Thanks everyone for their input. I agree that a change that removes the word 'any' from the the current drafting of D4.5 would be beneficial to clarify the current rule. 

It may also be worthwhile to discuss whether the D4.5 rule drafting (even including the discussed change) is optimal at all. Take this as an example,

3 Round Robins scheduled.
2 Completed
1 incomplete.
Teams A and B end up tied.
Team A won both races against B in Rounds 1 and 2.
Team B won the race in the incomplete 3rd round.

The current rule (or at least my understanding of it) says B comes out on top in the Tie Break.

Seems unfair to me. If the 3rd round had not started or had been finished all the rounds (be it 2 or 3) would have been used. But because it was incomplete it gets a heavier weighting. I don't understand why this happens.
Even if it was two rounds (1 complete, 1 incomplete) why does the incomplete round become 'special'?

Perhaps, the original intention was in the case of two AND ONLY TWO teams tied that all their races would be counted including the completed and incomplete rounds. Whereas, if there was 3 or more teams tied the incomplete round would not be used until the various tie break methods whittled it down to two tied teams and then the incomplete round would be included for those two teams.

I'll leave you with it.

Thanks again,
Ross.

I agree that it isn't a great system. I think the idea is that it gives weight to the final race between the teams. 

You could change D4.4(c) to be 'if two teams remain tied, the winner of the last race between them, including races in an incomplete round-robin. 

I am not a fan of D4.4(b) as teams racing should be about the win/loss not so much about the points the team has scored.  If there is an incomplete round-robin I would want it to count before we start tallying up points between teams.