I too have hit this rather common problem, which I suspect many of us first time Zynq users run into.
The example project for using an axi_gpio block worked fine, the first time. It was only after further experiments with Vivado/SDK/Zynq that I ran into other newbie issues and in frustration did a fair amount of 'delete and start over' debugging.
Eventually I got into a state where xgpio.h was no longer visible in my SDK project even though it had been earlier. I could see xgpiops.h but don't go down that rabbit hole - that's for the gpio module connected directly to the PS world.