I found that Chip_SCT_ClearEventFlag in sct15xx.h clears all pending events.
STATIC INLINE void Chip_SCT_ClearEventFlag(LPC_SCT_T *pSCT, CHIP_SCT_EVENT_T evt)
pSCT->EVFLAG |= evt;
SCT event flag register
This register records events. Writing ones to this register clears the corresponding flags
and negates the SCT interrupt request if all enabled Flag bits are zero.
OR-ing will clear the evt as well as all events which read as '1'.