That's going to have to be done manually. The bowler's average (and handicap if applicable) is based on the total games bowled, so BLS will need that number. But it should be a relatively easy thing to do manually. Since this bowler is known to have the first 12 games as a substitute, the bowler's total pins as of the 12th game would be subtracted from the season total pins, and the number of games would be 12 less than the final tally. Further, the average reported to the association at season end would also include all games bowled. If an average is a condition for an award presented by the association, the total season games would also be in play.
EDIT: I opened my BLS to check to see if there was anything relevant to this. Be sure to read this.
In Setup > Rules, going down to the "Special Recognition" tab, scroll down about 1/3 of the way. There are several divider lines; the area I'm focusing on has fields marked "Week final season standings and recognition are concluded". Below a second field, there is a switch labeled, "Should a temporary substitute join a team, do games bowled as a temporary substitute count towards the required number of games?" While I would set this to "No" anyway, my read on this switch is that it refers to game count, and not pinfall. To check this, I ran a test league with one team having the same bowler absent for four weeks, using the same sub throughout. For the fifth week and later, I rostered that sub onto that team and processed a couple more weeks. Once his name showed up as high average (I forced high scores), the average listed reflected every game bowled, and it didn't subtract out the first 12 games bowled as a sub. So as I stated in the beginning, you will have to do this manually.
Back to my original reply, this note regarding the USBC rulebook:
Do note that the CAQ mentioned 12 games as an example (I found it on page 37 of this year's rule book, found online via link at bowl.com. It may be that this bowler coincidentally has 12 substitute games, fine. We are at a point where a league starting immediately after Labor Day would have the appropriate number of weeks bowled by now for approximately 12 games to be the case. If he joined after the 9-game mark, naturally the thing to do would be 9 games instead of 12, or whatever number is the case.
Always check, download, and install the most recent update of your software to ensure that issues may have been corrected.