How does a renege that is discovered later in a bridge game affect the scoring?
Everything below still stands, but it now occurs to me that it may not address the correct aspect of the question.

The renege having been noted, and the appropriate penalty adjustment made as described below, the play of the hand is completed.

At this point the deal is scored according to the contract as originally bid, with the trick results as played and adjusted for the renege. If the contract is made, points below (and possibly also above in the case of overtricks) the line are scored by Declaring side; otherwise points above the line are scored by Defending side.

In this sense, if the determination of made or set was decided by the penalty adjustment for the renege, then said tricks can be said to be properly scored below the line. This may be the confusion that OP is originally inquiring about.



The Laws or Rubber Bridge (2014) clearly state:


  Law 64 – Procedure After Establishment of a Revoke
  
  When a revoke has become established,  
  
  
    A. if the offending player won the trick on which the
    revoke occurred, (penalty) that trick and one of
    any subsequent tricks won by the offending side
    are transferred  to the non-offending side (if no
    subsequent trick was won by the offending side,
    only the revoke trick is transferred).  
    
    (For the scoring of transferred tricks see Law 77.)
  
  
  Law 77 – Transferred Tricks
  
  
    A trick transferred through a revoke penalty is reckoned for all scoring purposes as though it had been won
    in play by the side to which it had been awarded.
    
    
      Example:
      
      Declarer plays in 3♥ and takes eight tricks. A revoke by a defender is found to have been established, with the penalty determined to be two tricks. Two tricks are transferred from the offenders to declarer, who therefore has 10 tricks. Since he bid only 3♥, he scores 90 trick points, which count toward game, and 30 premium points for the overtrick.
    
  


Note that Law 77 and accompanying example clearly states that the transferred tricks are transferred only in regards the play; not in regards the contract. This is consistent with the scoring described in Law 72 (my emphasis):


  Law 72 – Points Earned
  
  The result of each deal played is recorded in points,
  which fall into two classes: 
  
  
    A. Trick Points. Only declarer’s side can earn trick
    points and only by fulfilling the contract. Only the
    value of tricks named in the contract may be scored
    as trick points (see Law 81). Trick points mark the
    progression of the rubber toward its completion. 
    
    B. Premium Points. Either side or both sides may earn
    premium points. Declarer’s side earns premium
    points by winning one or more overtricks, ....