That is why they tried to get his emails to her excluded from the release by classifying them “executive privilege”.
They may have actually been successful too, since I haven’t seen any emails in the released ones with Obama on the recipient list. However, some of the released emails indicate that Obama does use email aliases as well, so he could be there and we just haven’t discovered his alias yet.
The FBI notes (302s) that were released by the FBI, when interviewing Abedin she was asked if she recognized a Alias used for Obama. Her first response was “isn’t this classified?”
So the FBI knew Obama was emailing Illary on her private system...