After your aircraft from B. to C. pushes back from the gate, at some point, the gate agent reconciles the pax list with the tickets-boarding passes which were pullsed as pax boarded the given craft. So if you were on the list, but your ticket was never "lifted" (inside term for taking your ticket) then the gate agent should take you off the final list of pax that boarded the craft. This process is often done in a room which is sometimes called Post Departure.
One reason the airline goes through this process, besides for the accounting reasons, is in the event the aircraft gets into an accident this way the authorities know exactly who was on board that airplane. In news reports re plane crashes, they will often speak of the process of reconciling the tickets with the pax list.
Even if you are e-ticketed, generally they will take/retain/lift some sort of boarding pass/authority as you board for the reconcile process. It's kind of like balancing your checkbook, e.g. you look at the notations on the statement, and then make sure you have xld checks for said notations/debits on the statement.
I have read anecdotes where a pax will actually board a flight (get their ticket lifted), and then later disembark from the airccraft. E.g. they might say they are going to use the facilities, make a phone call, etc........but they never board again. In this case, there would be a discrepancy in the pax list and the ticket lift count, vs. the hand count the crew does just before the plane pushes back. This may also impact weight and balance figures, though I'm no weight and balance expert.......so someone else will have to tell you whether/if such would ever have a real impact (probably 99% of cases no). As someone put it on this board once, until that aircraft pushes back, the gate agent doesn't really kno whose on first or whats in coach! I suppose in this latter board-disembark scenario you would stand a better chance of not having your name "offed" from the flight, because firuing out who "you" are would probably be more trouble than its worth the airline as noted on a domestic flight.