What do you mean by a high humidity environment? In my opinion, you should mention the drying conditions. Then we can discuss whether flavonoids and polyphenols may be affected or not.
It is normal for it to affect because you did not stop the work of the enzymes and some fungi can grow, and all of this will lead to oxidation and loss of the active substances such as polyphenols and others. But I advise you to do a drying process under a vacuum so that you can get rid of the water quickly and without destroying the plant tissues or oxidizing the active substances.
Yes, drying leaves and stems in a high humidity environment can influence bioactive molecules like flavonoids and polyphenols negatively. High humidity can lead to their degradation, microbial growth, loss of volatile compounds, and dilution due to higher moisture content. To mitigate the negative effects of high humidity on bioactive compounds during drying, it is often recommended to use controlled drying conditions with appropriate temperature and airflow.