The staff of Immigration in Bitung (Lembeh is a part of Bitung) is very friendly and helpful with visa extensions.I have not done this myself, but one month ago while staying in NAD Lembeh another guest and his wife extended their 30-day visa to a 60-day.
It seemed quite simple; they both went to the immigration office in Manado along with a member of staff from NAD. After a short 1 hour visit they both returned with extended visas.
I would suggest you talk to the staff in the place you are staying.