As far as i know the Gemoro in shavuos (2a-b see vaiant opinions of different tanoim) only goes as far to say that we need the Chatas offering brought on rosh choesh, yomtov and yom kippur, on behalf of the tzibbur to atone for sins which we knew about, then forgot that it was prohibbited, or knew of its prohibition then forgot about ones action.
Therefore "Lo yodim" (which is mentioned in vidui al chet on yom kippur) means we still don't remember those 2 stages of knowing then forgetting, on those sins Hashem atones us in the interim with the public sin offering which is substituted for our prayers as there is no Temple.
When we do remember those 2 stages, if it is a koreis punishment sin, then we bring our own private chatas offering, and the kid goat that goes to azazel (of the cliff) on yom kippur atones for other prohibitions in the same vein of having erred after knowing earlier that action was wrong (the kid goat off the cliff also it atones for intentional transgressions along with repentance for those sins) . This is "yodim" That we ask to be atoned through our prayers.
Some one who is completely unaware is not even a Shogeg (who errs) rather an oneis (faultless) of which it states: ואם בשדה ימצא האיש את הנערה המאורשה והחזיק בה האיש ושכב עימה וגו' ולנערה לא תעשה דבר" (דברים כב-כה). ולנערה לא תעשה דבר - מכאן שהאנוס פטור - Bava kamma 28b -" If the betrothed woman was found in the fields and was forced by the man etc. To the woman you shall not do anything" From here we see that someone who is faultless is exempt.
Bottom line is that our prayer nowadays are a replacement for the temple service and the words should not just be simply translated, they have deeper meaning.
This case seems to be that the involved person did their utmost to make sure not to eat insects to a satisfactory level of checking of rabbonim that no insect should have been present and is asking if something happened completely in absence of their knowledge whether they need a kapporo it would seem that no, as this would be categorized as oneis (faultless).