VBATT pin can be left not connected if not used.
Here is a problem on the BBS see solutions, VBATT not connection affect the JTAG use, I want to ask, will not affect the USB device enumeration.
The JTAG interface of FX3 does not work if the VBATT pin is not connected to a power supply. Although the JTAG interface is powered by the VIO5 supply domain, the internal architecture of the chip requires that the VBATT pin also be supplied with a valid power source.The underlying requirement here is that the USB domain of FX3 be powered. In bus-powered designs, it will be powered via VBUS; in self-powered designs, it needs to be powered via VBATT.