Don‘t even bother further with this design approach. It will never work.
If you need to revise your PCB anyway dot it right with a differential sensor.
My educated guess is that your two sensors are not on the same PCB but one is located within the box and the other outside because the Bosch sensors do not have hose connectors. This maens it is likely that either the power supply or the ambient temperature of both sensors vary when you switch on the fans. The imperfections of the temperature compensation for absolute pressure sensors alone easily explains the diverging of the measurements.