I am designing a landing pad for a drone that will have electromagnets built into the pad. My drone has a pixhawk 2 with PX4. I'm worried that the electromagnets in the pad will throw off the drone's IMU/magnetometer calibrations and affect it during flight. Does anyone have any insight into if magnets can have a delayed effect on a magnetometer/IMU like this? I obviously won't be flying while on the pad, so am only worried about its calibrations once in flight. Thanks!
Without knowing the specifics of the sensitivity of your magnetometer and electromagnet, it is impossible to give a concrete yes or no answer.
With that, in general any source of magnetic field is likely to cause some disturbance in a magnetometer measurement. This includes internal sources, such as the electronics and motors on the drone, or external sources, such as any magnets in the environment.
The calibration for a magnetometer can really only account for the internal disturbance sources and cannot account for any time-varying aspects of the internal or external disturbances.
My advice would be to perform your magnetometer calibration with it installed on the drone, but away from the platform. This calibration should remain correct until something on the drone is changed.
You may see disturbances when the drone is on the platform, but there should be no need to re-calibrate in this case.