You can keep practicing qigong. Your condition may change in relation to taking medication and doing qigong. You may become better, and not need the medication. This may be a gradual change. If you are going through changes, you might want to monitor yourself closer on the doctor side of things.
You have to coordinate that a bit, in terms of weening off medication, "if", that is the case. Also, in the meantime , you can put your energy/intention into the medication you are taking. Ask the higher spirits/master's energy to put what you need into the medication, and have what you don't need, to move through you (just like releasing a blockage). Use your sword fingers to put your prayer in, or just hold it up and visualize the prayer. Remember, in practice, the exercises are always balancing your body, as is...you are always better off doing qigong. Don't stop. You may adjust your focus if you have concerns. Inactive versus active.. Do what feels good. If medication is a question, you should talk with the doctor, but don't worry about practicing qigong. It isn't a time to yield, be an active participant in your self healing.