So, sorry if I'm missing it but did he complete all his scenes and they chose not to use them, or was it only partially completed when he died and therefore they had to reshoot the Fajo portions?
Not completely clear. What we konw:
-Episode was filmed in March. According to the TNG Companion, "a few days" into filming, Rappaport attempted suicide (the attempt was not successful).
-After this ATTEMPT, the TNG crew recast and reshot whatever scenes had already been made with Rappaport (it's not clear whether this was every Fajo scene, or only some. Each episode took, if I recall, about 6 days to shoot, so a "few days" could have been as much as 50% through filming, though not all these scenes may have been with Fajo in).
-Rappaport later successfully killed himself at beginning of May.