Jamie, I believe you are to take the score you most likely would've made.
Mr. Clayman I am aware that is what the Handicap Manual says, Section 4-1 Unfinished Holes and Conceded Strokes. There is also Section 4-2 Holes not Played or Not Played under the Rules of Golf, I will deal with that one in a minute.
First off, what supersedes what, The Rules of Golf or the Handicap Manual? Well, my amateur's reading of the Rules of Golf notes that Rule 1-1 says "The Game of Golf consists of playing a ball with a club from the teeing ground into the hole by a stroke or successive strokes in accordance with the Rules." Note the last 5 words.
We then move to deal with Section 4-1 by looking at Rule 2-4 "A player may concede his opponent's next stroke at any time, provided the opponent's ball is at rest.
The opponent is considered to have holed out with his next stroke, and the ball may be removed by either Side." Emphasis mine. So, THE RULES OF GOLF state that you holed out, in my case, IAW the rules of golf, I holed out for 2, because my opponent conceded stroke (he mostly conceded the hole, but in doing so, he conceded that my second shot was good). Now, according to the Handicap Manual, I have to run percentages through my head to figure out what I would have likely made on that hole. Now that's just fancy. Either way, you tell me which to follow, the Rules or the Handicap Manual. Reading Rule 1-1 makes it an easy decision for me.
Now, on to Section 4-2. This again uses most likely score, but brings handicap into the picture. Par plus handicap shots is applicable. There are two parts to this rule, one is holes not played, one is holes not played IAW the rules. Now, for the first part, assuming you are not playing match play, in which case the only way to not play a hole is for your opponent to concede you a 1 on the tee, you are playing stroke play. Well, Rule 3-2 says "If a competitor fails to hole out at any hole and does not correct his mistake before he makes a stroke on the next teeing ground or, in the case of the last hole of the round, before he leaves the putting green, he is disqualified." So, simply put, any round in which the player does not hole out, other than in match play, is an invalid round, therefore ineligible for handicapping, or so says the rules. To the second point, holes not played IAW the rules, well, for that we must look at Rule 1-3 Agreement to Waive Rules "Players must not agree to exclude the operation of any Rule or to waive any penalty incurred." Penalty=DQ.
So, if following the Rules of Golf, if you fail to hole out or fail to follow a rule intentionally (or unintentionally and fail to correct it prior to completing your round or teeing off on the next hole depending on the situation) you are disqualified from your round and it becomes invalid.
Once again, which book reigns supreme, The Rules of Golf or The Handicap Manual? Like I say, play every shot of every round in strict accordance with the Rules of Golf and none of this handicapping manual nonsense is needed, and by the way, I still say the average handicap would go up at least 5 shots if everyone played every round IAW the rules.