For a few generations germ theory and generally all usual modern medical knowledge prevailed. However with the loss of microscopes and other equipment soon suspicion and conspiracies arose when the "medical people" couldn't prove their beliefs anymore.
"You really want me to believe that there are small invisble demons that cause illness? And they are everywhere? How should me washing my hands help then if the demons are also on the towel that I use to dry my hands. That's just silly!" Hygiene declined and people started to counter scientific medical knowledge with anecdotical knowledge "I never wash my hands and I get barely ever sick".
Even some medical personel started to question the germ theory.
Birth of a religion
With public health on the decline a few doctors, theologists, philosophes and others started faricating a religion based on modern medical knowledge. It contains a lot of rituals like washing your hands before a meal to not offend the god of food or calming the godess of surgery by emptying a bottle of whisky on the spot where the cut is planned. CPR becomes a prayer to not take the soul of your loved one while help is on the way. Also some other professions joined in and tried to preserve their knowledge when the possibility to demonstrate the foundation was gone. While others like mathematics and construction engineering did not have such problems and could just continue their work and studies (though without heavy machinery). The philosophes and theologists helped in fabricating the religion in a way that it has the potential to survive millenias without being overtaken by other religions.
Spread of the religion
At first the newly founded religion is laughed upon (like most new religions) but within a few generations it became clear that those who followed often got the promised long and healthy life. 1000 years after the disaster the religion has risen to dominate the planet. By now only a few leaders know that the holy manuscripts where man-made and still maintain a big part of the knowlege of old. Within the next millenias the clergy introduced their own ideas into the religion mainly to grant themselfs more power.
After 20,000 years the knowledge of the creation of the state religion has long passed, even the head of state and religion, the "pòpér" doe not know that their religion was made by ordinary man. A lot of rituals still implement modern knowledge but most have changed in focus or even completly lost the most important parts.