Although the Torah only discusses bringing a Pesach Sheini for those who were ritually unclean or were far away from the Temple (the only place offerings can be brought) for the Korbon Pesach, the Talmud (Pesachim 93a-b) discusses the requirement to bring a Pesach Sheini even if there was a different reason why the first one wasn’t brought. The terms used by the Talmud are “hizid,” meaning he purposely didn’t bring the offering even though he could have and knew that he should have, and “shagag,” meaning even though he could have brought it, he didn’t know that he should have (e.g. he forgot which day he was supposed to bring it). The Talmud quotes a three way dispute between Rebbi, Rabbi Nasan (R”N) and Rabbi Chananya ben Akavya (RChBA) regarding when someone deserves “Kareis,” one of the most severe punishments (meted out by the heavenly court, not human courts), and the punishment described for not bringing the Korbon Pesach and/or Pesach Sheini (see Bamidbar 9:13). There are numerous issues that this discussion raises; I would like to focus on just one (or two) of them.

With two separate offerings being discussed (Korbon Pesach and Pesach Sheini), two causes for not bringing them (purposely not bringing it or inadvertently not bringing it), and three opinions that are to be applied to each possibility, twelve scenarios are covered. Nevertheless, since everyone agrees regarding two of the scenarios, and two agree (albeit a different two each time) on the other two scenarios, the Talmud is able to sum up what everyone holds in just over five lines of text. Still, with the rationale behind each opinion being different, explaining all twelve (or at least trying to read someone trying to explain them) can be a bid tedious. I’ll try to simplify it as best as I can, in order to explain the specific difficulty I want to address.
Rebbi is of the opinion that each offering represents its own individual “holiday,” so purposely not bringing either of them (when required to) deserves the punishment of “Kareis.” Therefore, if one purposely didn’t bring the first, or purposely didn’t bring the second (again, discussing only situations where one was required to bring each, as opposed to, say, when one is ritually unclean, so is not allowed to bring it, or when someone brought the first one so has no need to bring the second one), “Kareis” applies. (Rashi points out that since a person can only get “Kareis” once, even if a person purposely doesn’t bring both, only one “Kareis” can apply.) It is only when both were inadvertently not brought that a person who didn’t bring either escapes this punishment. (In this situation, all agree that there is no “Kareis.”)
According to Rabbi Nasan, even though the second offering serves as compensation for not bringing the first offering, bringing it does not repair the damage done by not bringing the first one. Therefore, even if the second one not being brought was done inadvertently, the “Kareis” from purposely not bringing the first still applies. On the other hand, if he inadvertently didn’t bring the first one, he cannot be given “Kareis” even if he purposely didn’t bring the second one, as (according to R”N) the punishment of “Kareis” only applies to the first, not the second.
Rabbi Chananya ben Akavya understands the Pesach Sheinu as being able to fix the damage that was donethe first time, with “Kareis” only coming if he purposely didn’t do both; if either the first or second (or both) were missed inadvertently, there is no “Kareis.”
For obvious reasons, the Talmud does not discuss what happens if someone did bring the Korbon Pesach, as once the mitzvah was fulfilled properly, there is no need to bring a Pesach Sheini – and there can be no punishment for not doing so. However, the Talmud also doesn’t address what happens if someone brought the Pesach Sheini, i.e. whether doing so removes the “Kareis” that purposely not bringing the Korbon Pesach brings. True, we know that according to RChBA bringing the Pesach Sheini means there is no “Kareis,” but what about according to Rebbi and R”N? Why doesn’t the Talmud discuss this possibility (and its ramifications) as well?
Although this question is well worth discussing in its own right, the question that led me to this topic was what the Rambam, who follows Rebbi’s opinion when he codified the law, says about such a case. In Sefer HaMitzvos (Positive Commandment #57) he writes “it is also true according to Rebbi that if he purposely didn’t bring the first one [even though] he brought the second he deserves [Kareis],” while in Hilchos Korbon Pesach (5:2) he writes “if he purposely didn’t bring the first, he brings the second, and if he did not bring the second, even inadvertently, behold he deserves Kareis,” with the (strong) implication being that he only gets “Kareis” for purposely not bringing the first if he doesn’t bring the second (whether his not bringing the second is done purposely or inadvertently). How can what the Rambam wrote in Sefer HaMitzvos be reconciled with what he wrote in Mishneh Torah/Yad HaChazaka? Does a person who brings the Pesach Sheini still deserve “Kareis” for purposely not bring the Korbon Pesach or not?
Some (including the Rambam,’s son, Avraham) simply push the question aside by saying that the Rambam’s opinion changed between the time he wrote his Sefer HaMitzvos and when he wrote the Yad HaChazaka. However, the possibility that there is more than one possible answer to the question of what happens if someone brought the Pesach Sheini after purposely not bringing the Korbon Pesach makes the question of why the Talmud didn’t discuss such a scenario that much stronger. It is alsomuch more difficult to classify the two offerings as separate and distinct “holidays” if bringing the second can fully compensate for not bringing the first. (Although they are connected in the sense that bringing the first prevents an obligation to bring the second from applying, that is not the same as bringing he second fixing the damage done by not bringing the first.)
Rashi (Pesachim 93a, d”h Tashlumin d’Rishon) says explicitly that, according to R”N, one gets “Kareis” for purposely not bringing the Korbon Pesach even if he brings the Pesach Sheini. Later (93b, d”h l’Rebbi ), Rashi tells us that the reason, according to Rebbi and R”N, one still deserves “Kareis” if he purposely didn’t do the first even if his not doing the second was only inadvertent is because the second does not “fix” what the first one “broke.” If the second doesn’t “fix” what the first one “broke,” and one of the things “broken” by purposely not bringing the first one is deserving “Kareis,” then even if one brought the second one, what was already “broken” remains “broken,” i.e. he still deserves “Kareis.” (If anything, that inadvertently not doing the second one doesn’t “fix” purposely not doing the first one is learned from the assumed fact that he deserves “Kareis” even if he brings the second one!) In other words, by telling us that inadvertently not bringing the second does not remove the “Kareis” brought on by purposely not bringing the first, the Talmud is also telling us that according to Rebbi, who considers each of the two offerings as separate “holidays,” and R”N, who also does not consider the second to be able to “fix” the first, the same is true even if they actually brought the second one. And since we know that according to RChBA one does not deserve “Kareis” unless he purposely didn’t bring both, there is no need to discuss what happens if one purposely doesn’t bring the first but brings the second.
The Rambam (Hilchos Pesach 1:2) tells us that anyone who purposely does not bring the Korbon Pesach deserves “Kareis,” without providing any qualifications. If it were true that anyone who brings the Pesach Sheini does not deserve “Kareis,” the Rambam should have mentioned this here, when telling us that not bringing the Korbon Pesach carries the punishment of “Kareis.” The question we are left with is why the Ramban implied (in 5:2) that if one brings the Pesach Sheini he doesn’t get “Kareis.”
The Yad HaChazaka was written in order to make it easier for people to know what the conclusions of the Talmudic discussions were without having to learn through the entire Talmudic discussion. He took a lot of heat for this, but it is clear that his intent was not for those who are learned, or who could become learned, to disregard the Talmud and just rely on his conclusions. Rather, he expected those who could delve deeper into the Talmudic discussions to do just that (even if they used his work as a reference to see what his conclusions were). His main audience, though, was the layman, who wasn’t going to (or wasn’t able to) learn the entire topic and figure out what the Talmud’s conclusions were on his own.
For this audience, writing explicitly that there is “Kareis” for purposely not bringing the Korbon Pesach even if the Pesach Sheini was brought might dissuade them from bringing a Pesach Sheini (under those circumstances), as they might think there is no reason to bring the Pesach Sheini if they deserve “Kareis” even if they do. Instead, the Rambam focused on the fact that purposely not bringing a Pesach Sheini when required to deserves “Kareis” in its own right, so that they would realize the seriousness of not bringing it when required to. Just as the Talmud relied on our ability to figure out that according to Rebbi (and R”N) “Kareis” is deserved for purposely not bring the Korbon Pesach regardless of what happens with the Pesach Sheini, the Rambam relied on those who can delve deeper into his words figuring this out as well, especially after almost spelling it out at the beginning of Hilchos Pesach.
[As far as the implication in Sefer HaMitzvos that only according to Rebbi does one who purposely did not bring a Korbon Pesach deserves “Kareis” even if he brings a Pesach Sheini, the word “compensation” used does not mean the same thing as it does when the Talmud in Pesachim uses it in contrast with “fixing,” but the “compensation” discussed (Chagiga 9a, Hilchos Chagiga 1:4) in regards to bringing a Chagiga that should have been brought on the first day of Yom Tov on one of the next sis days instead. That “compensation” is not considered a separate mitzvah (when enumeration the 613); Pesach Sheini is.]
Are his words (in 5:2) misleading? Yes, and perhaps purposely so. But he followed the Talmud’s lead, and felt he didn’t need to state explicitly (especially if doing so could be detrimental) that one who purposely didn’t bring the Korbon Pesach deserves “Kareis” even if he brings the Pesach Sheini. In Sefer HaMitzvos, on the other hand, which was designed for the more learned (as evidenced by the complex “Sh’rashim” he lays out to explain how he chose which mitzvos qualify, complexities he refers to often when listing the mitzvos, including this one), he was explicit about it. And he countered (preempted?) his misleading implication in 5:2 by stating, without any qualifications, that anyone who purposely does not bring the Korbon Pesach when they are required to deserves “Kareis.” Anyone. Even if they bring the Pesach Sheini a month later.