Metabolic ward studies are the gold standard because they control all variables. Unfortunately they are costly and it would be unethical to do them long term (you have to keep people couped up).
That's why you don't find long term studies of this nature.
However long term studies are generally plagued by inaccuracies, such as self reported dietary intake, poor compliance and other issues.
Also it does not take 3 weeks to become keto adapted. This study:
https://www.ncbi.nlm.nih.gov/pubmed/24351673/ shows it can take as little as 48hrs.