First off, even if the humidity is at 99% no need to worry Having high humidity such as 80-90% temporarily (a few days to a week or two) is totally fine. BPs would be exposed to these conditions normally in the wild after rainfalls and whatnot, and when in shed, some snakes will stay in their humidity box for a week, and the humidity inside those can be 90-100%. Overly high humidity is only a problem if it is a chronic problem and if the enclosure is unsanitary, which would lead to bacteria growth. For the most part though, the problem people have is too low humidity, not too high.

It's normal for bedding to dry out after it's been in the enclosure for a while (and also normal for cypress mulch to be very wet when it first goes in—humidity goes up to 90% for me if I do a full bedding change). I use a tub that holds humidity pretty well so I mist once or twice a week to keep it at 55-65% unless my BP is in shed (then I mist more and go up to 70-80%).

Has the humidity gone down since you posted this? I can't imagine it staying at 99% for more than an hour especially with a glass tank with a screen top, so if it stays at 99% for a few hours I'd suspect something is wrong with it. I can't imagine a humidity gauge going up to 99% unless you deliberately soaked it. Could you take the thermometer/humidity monitor out of the enclosure and let it sit in your room or outside where you know what the humidity should be (you can see daily humidity on the weather forecast) to see if it's roughly accurate?

Is your screen top covered by anything? It should be partially covered to maintain humidity but it also shouldn't be so closed off that there is no incoming air supply or ventilation. Overall I don't think you could make a glass tank too humid for a ball python unless you cut off too much airflow.