To understand this, we must preface who Rav Sheishet was in his Giglul. Know, that 'Baba Ben Buta' the Chassid, who was a student of Shamai haZaken, spent all of his days as a korban safek ('אשם ספק'). When he returned now in a gilgul as Rav Sheishet, he did so to complete whatever particular rectification he needed to (to fix whatever small damage he did), and when King Hordus took out his eyes in his previous life, so too in this life, (Rav Sheishes) was also blind.
This [connection between the two of them] is also seen in the letters of their names. With this, we'll come to the explanation -- know that what rectification one does not complete in a first gilgul, he is required to reincarnate again to complete it, even if it is for something small that is missing. Here, if in the first gilgul he completed [the rectification] of his Nefesh, but he was only missing a small thing, when he returns in his second gilgul, all of the reward of the Torah and mitzvot that he does now in this second gilgul, it is for the benefit of his Nefesh (which was rectified in the first gilgul).
So when he comes now into the second body to complete [the minor thing missing], when it comes for a body to rise in Techias HaMeisim, his Nefesh will return to the first body with which he toiled in Torah and mitzvot, as was required of that body (to rectify his Nefesh). He does not return to this second body; he only borrowed it (this body will only rise with the specific nitzutot which were connected to it.
Thus, Rav Sheishet knew that his Nefesh was already in the first body of Baba Ben Buta; that he was a great 'Adam' in the Torah and he was a well known chassidic celebrity, and that he did not return to reincarnate into this second body except to borrow it for a small item that he was missing. Thus, his [second] body was sad about this, because for him (Rav Sheishes), the Nefesh in his body would be taken by the other body (that perfected it), and in the end (at the time of Techias HaMeisim), his Nefesh would go and return to the first body.
So it was, in a way, that all of what he did as far as his toiling in Torah study was not meant for the happiness of his body, and with this, he said, "חדאי נפשי וכו'", and not for me (not for my body). Rather, all my efforts I do for you (for his Nefesh which will belong to the other body), and not for me.