Change the front wheel Skewer. I had the same issue, the noise was there, then not. Sometimes after 10 mins showed up, suddlenly stopped, then shoed up again. I even thought the frame (or the fork) had an internal crack or something.
After retighten BB, Bolts, changed the stem, greasing all posible places where the noise could be generated a friend suggested to change the from quick release... I found a QR that had probably 20 years old, and no more noise EVER!... Put an old steel QR if u have one, I bet the noise will go away. Just in case my frame is carbon. Hope yours is carbon also. THe problem is that carbon is really good sound conductor so sometimes a sound that is generated in the back of the bike for example it will be louder in the BB shell...
Hope this fix your problem