The answer to this question can be found in a Meshech Chochma in Parshas Shoftim.
There is a well known machlokes between the Rambam and the Ramban (Sefer Hamitzvos Shoresh 1) about the nature of dinim d'rabbanan. The Rambam holds that all dinim d'rabbanan are based on lo tasur. In other words there is a chiyuv d'oraysa to listen to them. The Ramban asks an obvious question, if so why do we say safek d'rabbanan lekula? After all, if you violate a d'rabbanan you are violating the issur d'oraysa of lo tasur?
The Meshech Chochma (Devarim 17:11) explains the Rambam as follows. He says that every din d'rabbanan is not necessarily a fulfillment of the will of Hashem. The proof is that the Rambam paskens based on the Gemara that a later greater Beis Din can be mevatel a takana of an earlier Beis Din. If every takana was the will of Hashem how could that be? Therefore, he explains that by dinim d'rabbanan what is not important is the actual mitzva act, but the fact that you listened to the Chachamim and did not rebel against their words. The issur of lo tasur is an issur to rebel against the Chahamim, to not listen to them. Given that, we understand why sefeka d'rabbanan lekula because the act of doing the mitzva is not the main point, the point is listening to the chachamim, once it is a safek, there is no need to do the act because it is not so important (contrast that to a mitzva d'oraysa where the act is clearly an unequivocally the ratzon hashem).
Based on the above, it is clear that there is no need for teshuva on an issur d'rabbanan b'shogeg. If the whole idea of dinim d'rabbanan is to listen the chachamim and not rebel against them as the Meshech Chocham explains, then by definition an aveira d'rabbanan b'shogeg is not a problem, you did not rebel, you did not know that you were doing an issur and therefore there is no need for teshuva.