What you are describing is remotely possible for it to be your body healing…but highly unlikely.
In all probability, what you are describing are Qi Gong side effects indicating you are practicing wrong or doing a type of Qi Gong that is not compatible with your body or emotional state.
I would recommend you to change methods AFTER you stop for a week or two.
If it is a Qi Gong side effect, continuing what you are doing will eventually lead to damage to your overall health. This is one of the reasons that correct training and the guidance of a teacher is required. Even better is the guidance of a teacher who is a doctor of Traditional Chinese Medicine (for example, most people can do Qi Gong method XYZ, person A has asthma, person A tries Qi Gong XYZ and he has asthma problems, continuing on could be fatal, checking with teacher, he is told to continue, checking with TCM doctor, he finds that before he can do Qi Gong XYZ, he must do another type of Qi Gong to tonify his lungs).
The stopping is required so your body can have time to stabilize and return to a balance.
Changing methods is probably a good idea but if not that, you may consider trying shorter sessions and working up even more slowly than you think you should.
Also, not everyone is cut out for sitting or still Qi Gong. IT is one of the most common forms of Qi Gong, but there are some people who do not work well this way and MUST do moving Qi Gong. For example, I had a classmate who was VERY hyper. She was never taught still Qi Gong because she would have been a prime candidate for problems. I would have been an unnatural state for her to TRY to be still.
I never knew this topic was so complex until learning from my current teacher who is a doctor of TCM and one of the founding teachers of one of the major colleges of TCM in China as well as a martial arts and Qi Gong master of some renown.
Even with his training, I have been instructed on which types of students to avoid teaching due to potential medical problems. All of this after over a quarter of a century of training.
Exercise caution. Feelings that are unpleasant in Qi Gong practice are almost always indicators of bad things.