How to erase a bitstream from an FFPGA using a microcontroller?
The JTAG commands required to program or erase the FPGA are defined by IEEE Std 1532

https://standards.ieee.org/findstds/standard/1532-2002.html

The manufacturere should provide a BSDL file that defines the command set for your specific FPGA.  Having both the BSDL file the IEEE 1532, and the IEEE 1149 standards should together provide all the information required to send the 

You first need to send the ISC_ENABLE command to enter programming mode.  Then send ISC_ERASE, to erase the portion of flash memory.then ISC_DISABLE when you are done.