However, it is not the same concerning [what happens in] 'Yibbum', and the reason for this is that reincarnation happens for reasons other than committing aveirot (sins) of the Torah. For aveirot, there is a rectification [for his sins] which come through hardships and suffering in this world or gehinom. [If the sins came through violating a certain negative mitzvah], then all of the [rectified] parts of his Nefesh do not require gilgul.
Rather, they can come with him having the status of an Ibbur, as we already described. So too with the sparks [that were already rectified in a previous lifetime -- they can come with him having the status of an Ibbur]. However, one who comes through the secret of Yibbum, this happens because he died without children (he did not do the mitzvah of 'Pru u'rvu' of having children, which apparently is required in every lifetime).
Thus, he is as if his efforts [in his previous lifetimes] were for nothing; it is as if he was never in this world, and it is as if his previous body never existed, as we learn in the Zohar, Parshat Vayeshev. Therefore, his Nefesh that was in the first body (which died without children), and all of its parts reincarnates completes now as if it is a completely new entity [referencing Ch.2, where a body is born with a Nefesh, Ruach, Neshama; and if he damages the Nefesh with a sin, the unblemished Ruach cannot rest on a damaged Nefesh, so the two cannot be together in this lifetime until he reincarnates and fixes the blemish in his Nefesh from whatever sin he did].
This [child born via Yibbum now can reset in this] second body; this second body becomes his primary body, and if he rectifies it [meaning, if he fixes the issue he created in the first body of dying without having children], then when he dies from this world, in the time [of Moshiach] when techias haMeisim happens, his Nefesh will return [not to the first body, which I assume did not have any serious aveiros which would require gilgul] but to this new second body [which he acquired through Yibbum].
However, the Ruach which was in his first body [has its own interaction between the original husband, his wife, and the new husband and his Ruach; this is not covered yet in the text], goes according to what is written in בסבא דמשפטים. So to explain this part, there is a difference between someone who dies without children, and comes into a new body via Yibbum, and someone who dies (having other aveirot of the Torah) that comes back via gilgul (reincarnation), and not via Yibbum.
Also here, recall everything we discussed about a Ruach and a Neshama comes into a body through what we explained concerning 'sparks' (nitzutzei) of the Nefesh.