I thought I'd share this and perhaps get an explanation. Was struggling to get CySysPmHibernate to wake and reset on a GPIO interrupt... turned out the issue was my high frequency clocks were set to ECO rather than IMO. But I'm wondering why this is - after all Hibernate stops all clocks (AN86233 3.3.2 ), so why would the GPIO interrupt require the clocks configured that way to operate and wake up? This is with a CYBLE-022001-00.
The hibernate mode is exited via a reset caused by the GPIO interrupt. Did you specify sync or double sync for the input? That might not work. Otherwise I would suggest you to contact Cypress directly: At top of this page select "Design Support -> Create a Support Case" and describe your problem.