I usually centrifuge the nano-emulsion, take out the aquaous media and add same vol. of methanol followed by vortex and ultrasonication. A clear supernatant sol. of methanol was obtained after centrifugation. Finally the phenolic and flavonoid content was determined using Folin–Ciocalteu reagent and aluminum chloride method respectively in methanoic solution. But the problem is everytime a turbid solution was obtained and finally unable to take the O.D spectrophotometrically.
As far I see in the original source of the method, your problem is connected with probably higher basicity of some solution:
Article Analysis of Propolis: Some Parameters and Procedures for Che...
https://www.researchgate.net/file.PostFileLoader.html?id=56e7bc5d40485449e6223f71&assetKey=AS%3A339806593798145%401458027613155
Determine the distribution of flavonoid between oil and water into emulsion is a difficult task. To determine the total content of flavonoid in the emulsion, it is necessary to await the emulsion stratification, and then spectrophotometrically determine the flavonoid content in the aqueous and oil phases.
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