Hi, Eugene,
I have asked the AE team, this is the intrinsic feature of the LPC55xx family rather than a bug.
You observed that the GPIO output pin loses it's logic and becomes input mode during power-down mode and deep power-down mode, the phenomenon can be explained by the power supply internally. The GPIO module is powered by PD_CORE power domain, after power-down instruction is executed, the PD_CORE power domain is lost, in other words, the GPIO module is power off. After waking-up, the PD_CORE power domain is recovered, so you have to reinitialize the GPIO module. Pls refer to page Power Domain : 1. CORE (PD_CORE).
The SYSCON and IOCON modules are powered by the PD_SYSTEM power domain, after power-down instruction is executed, the PD_SYSTEM and PD_AO power domains are valid, in other words,you do not need to initialize the SYSCON and IOCON modules after waking-up from power-down instruction.
I attach the Power Domain doc, hope it can help you
BR
XiangJun Rong