1. When a plant from higher altitude is grown or when its seed is cultivated in lower altitude, there will be a climatic change stress on the plant. This will naturally induce the plants to produce secondary metabolites. (Eg. Apples grown in higher altitude is more reddish than grown in lower altitude).
2. A metabolite produced to adapt to the environment and sunlight exposure will not be produced in the same amount when grown in lower altitude. (You can try with legume plants which are fast growing and you can see the result in not more than 1 month)
3. If you wish to extract the same yield as you get from plants in higher altitude, you can try micro propagation of plants using plant tissue culture
i think that metabolites in general, at the beggining will change their concentration as a process of aclimatation, because when you move them to a different microclimate they must to adapt to hte new habitat; in consequence they will change the metabolites production. also, secondary metabolites is known that are produced by plants when they confront hostil weather conditions.
I believe the key to the answer is in the evolutionary or physiological significance of the metabolites. Were they produced as a response to stress or as a result of the promotion of certain processes that are influenced by changes in the environment such as light intensity, quality and duration; temperature, pressure, [CO2] etc? If these metabolites are a response to stress conditions prevalent at high altitudes, reversion to low altitudes may reduce the concentrations produced. In the same vein plants from high altitudes may produce less at low altitudes. However this still needs to be validated by appropriate experimentation