"net-net" is not a commonly used phrase, and I would not recommend you start using it. Short answer: In this case, it probably means "total". Long answer: Net migration would refer to the total migration of something in or out of an area. Net net migration probably refers to the total after additional factors are added or subtracted. For example, you might say the "net migration of Canadian birds into the United States," referring to exactly how many birds crossed the border from Canda into the US and subtracting the number of birds that crossed from the US into Canada. "Net net migration of Canadian birds into the United States," might also subtract the number that died during the migration and are not alive today, and add the number that were born of parents who came from Canada this year.

I first read your question, I thought 'net-net' would probably something like birds move from their 'nest' to a newly-built 'nest'.