For cereals, I know that there is a difference between oven-dried moisture results and  NIR moisture results probably because oven dried moisture level will take into account both the surface and internal moistures of the milled grains. If that is the case, dry weight basis will be different. 

In oven dying volatile component of food is removed at high temperature which leads loss of dry matter and reduces dry weight. But in case of freeze drying only water  is removed by sublimation process and maintain the volatile components such.

Oven drying operations are accomplished at a higher temperature unlike in lyophilizer. Therefore, in oven drying, loss of volatile food component may  occur and depending on the oven drying temperature, further losses may occur due to the decomposition of carbohydrate, oxidation of fat and denaturation and coagulation of protein in the food sample unlike in the lyophilizer. The dry weight value of oven drying and lyophilizer are most likely to differ.

You should follow the standard method usually used in your field.