The practice of mindfulness meditation involves accepting “whatever is” in our present moment condition.
We may be sick or coughing; we may have the flu or even chronic body pain. Through meditation, we learn to view our experiences come and go, intensify and soften and then we get to watch them turn into something else.
Typically during meditation, we follow the breath because it is a convenient way to be aware of yourself. Breathing is rhythmic and central to life, so it’s always there, in your body, and is a great place to focus your mind.
So, when it is difficult to breathe, just observe “what is” pay attention to it and work on it in a compassionate and gentle way. Do the same as always, but instead of free and flowing breath, you will be stuffed up. You’re still breathing, right? Just differently than usual. Be aware of the differences and don’t judge it as good or bad.
Not every meditation practice is comfortable just as not every moment of life is. What we are doing when meditating is practicing getting comfortable with the uncomfortable.