The pins status will be similar to those of the FX3 during boot. The pins number & functionality may change, but the pin status will be based on the pin functionality and the selected boot-mode. Please check the attached doc for FX3 (table 31) http://www.cypress.com/file/201991/download
After the boot, the status will depend on what you set the GPIO value to be (i.e. it will be firmware controlled).