The purified natural extract when dried with vacuum oven becomes dark in colour whereas the same extract when freeze dried gives colorless product. Even though the vacuum oven drying was carried out at ambient + 10 degree celcius temperature.
Obviously, this (I mean 20 to 30 °C) is to warm in comparison to the conditions of lyophilization, where of most of the time the sample is disctintyl below 0 °C.
You should change to this method to avoid oxidation, and not work further with your oven.