Hi, there is no issue resetting the EKF between each flight, however you could maybe avoid this if you reduce the thresholds of the magnetometer checks (so the EKF won’t try to fuse the mag when the mag is affected by high current).
see EKF2_MAG_CHECK, EKF2_MAG_CHK_INC and EKF2_MAG_CHK_STR.
You can check in the log the values of estimator_status.mag_inclination_deg and estimator_status_mag_strength_gs during charging to set the thresholds accordingly.