Activities involving a secure element (SE) in a mobile device include a background operation. When the SE initiates the background operation, it informs the mobile device of an estimated duration. The mobile device thus recognizes that the SE is not in a stuck state, and maintains a clock signal and a power flow to the SE. Firmware updates to the SE include erasing a non-volatile (NV) memory in the SE in parallel with firmware or software updates to other processor systems in the mobile device. Needed data, for example calibration data or cryptographic key data, is preserved by storing data from some processor systems in one or more supplementary security domains (SSDs) in the SE. When a given processor system completes a firmware update, the needed data is restored to the processor system from the SSD.