Rava says that the sair hanasa bphnim is magen on issurim. My question is till Yom kipper what does he do to magen on issurim. If the averia happened on succos for example he now has to wait 11 and a half months till the cohen brings the sair...
Your question is equally relevant to any Lo Sa'aseh that one transgressed (which is not the subject of this Sugya); after one does Teshuvah, he must wait for Yom Kippur to complete the atonement, as the Gemara in Yoma teaches.
The answer is that it is only on Yom Kippur that one is judged for the sins of the past year, and thus it is at that moment that one becomes liable for punishment. Provided that one has done Teshuvah, Yom Kippur will atone for the sin, and the punishment will be averted.
In other words, between the time that one sins and the arrival of Yom Kippur, no judgement will take effect anyway, and thus no punishment is due.