YEVAMOS 98 (14 Sivan) - Dedicated by Doug Rabin in memory of his mother, Leah Miriam bat Yisroel (Lucy) Rabin, in honor of her Yahrzeit.

1) THE REASON WHY A "GER" MAY NOT MARRY HIS RELATIVES
QUESTION: The Beraisa states that a Ger who was conceived before his mother converted ("Horaso she'Lo b'Kedushah") and born after his mother converted ("Leidaso b'Kedushah") is prohibited from marrying his maternal relatives, such as his sister from his mother, or his mother's sister. He may marry only his relatives from his father's side.
RASHI writes that the Rabanan prohibited the Ger from marrying his maternal relatives because if the Ger would be permitted to marry his maternal sister who was born before his mother converted, he might think that he is permitted to marry his maternal sister who was born after his mother converted. Such a marriage, however, is forbidden mid'Oraisa by the Isur of "Achoso."
However, Rashi earlier gives a different reason for why the Rabanan prohibited the Ger from marrying his maternal relatives. The Gemara earlier (97b) relates that Rav Sheshes prohibited the two sons of Yudan the maidservant from marrying each other's former wives (their sisters-in-law), even though the brothers were conceived and born before their mother converted. In that case, the reason for the prohibition could not have been a concern that they would permit themselves to marry siblings from their mother born after her Gerus. Since they were born before the Gerus they would not be related to any children born after the Gerus. Rather, they were prohibited from marrying their maternal relatives because, as Rashi there explains, people might mistakenly think that just as a Ger is permitted to marry his brother's wife, an ordinary Jew may also marry his brother's wife. This reason -- that people will confuse the laws of Arayos of a normal Jew with the laws of a Ger -- applies to the case of the Gemara here as well. Why does Rashi here give a different explanation for the prohibition? (TOSFOS DH Nasa)
ANSWER: Rashi understands that the prohibition which the Gemara here discusses cannot be based on the same reasoning as the prohibition in the case of the sons of Yudan the maidservant. The Beraisa specifically discusses a Ger born after his mother converted ("Leidaso b'Kedushah"). The implication of the Beraisa is that a Ger born before his mother converted would not be prohibited to marry his relatives, and the concern that people might confuse the Ger with a normal Jew does not apply to prohibit the Ger from marrying his relatives. (Tosfos has difficulty with the wording of the Beraisa and offers numerous solutions for it, but Rashi's explanation avoids Tosfos' question entirely.)
Why, though, does that concern not apply in this case?
1. RAV ELAZAR MOSHE HA'LEVI HOROWITZ suggests that the concern that people might confuse the laws of a Ger with the laws of a normal Jew is reason only to prohibit a Ger from marrying his relatives l'Chatchilah (such as in the case on 97b). The Beraisa here, however, states that a Ger who marries his sister must divorce her even b'Di'eved. This stringent ruling is due to the Gezeirah that he might think that he is permitted to marry his sister born after their mother converted.
2. Rashi may understand that the concern that people will confuse a Ger with a normal Jew does not apply to natural relatives, such as one's sister. Every Jew knows that one is forbidden to marry his sister (see Shabbos 145b, Sanhedrin 7b). Only a relative through marriage, such as one's sister-in-law ("Eshes Achiv"), is subject to error; a Jew might mistakenly think that he is permitted to marry her when he sees that a Ger is permitted to marry such a relative. Accordingly, the reasoning which Rashi mentions earlier (97b) does not apply in the case of the Beraisa here.
On the other hand, the concern of the Beraisa here -- that the Ger will mistakenly think that he is permitted to marry his sister born after their mother converted when he sees that he is permitted to marry his sister born before their mother converted -- applies only to natural relatives. The Rabanan did not institute such a Gezeirah for a relative through marriage, as Rashi writes later (98b, DH u'Mutar). Thus, the two different prohibitions complement each other.