Is it possible to fix a corrupted flash? Error (209025): Can't recognize silicon ID for device

After intensive testing, I found out, that PCIE is working. I ran demonstration codes via batch and cpp files and I was able to retrieve some status info from the FPGA. I want to explore the PCIE capabilities a bit further but I face a problem. I dont know the addresses of the GPIOs. I would like to write some test codes (including buttons, leds, switches and other GPIO that are routed to the external connectors), based on the provided AVMM library/framework. But digging through all of the datasheets I could find, there is no information about ,,USER BAR" ,,ON CHIP MEMORY ADDRESS", ,,MEMORY SIZE" concepts (picture bellow is taken from the main datasheet, chapter ,,PCIe Reference Design for Windows".) Can you provide any more information, how can I adapt the manufacturer's example PCIE codes to do operations on all available GPIO pins? Also there are some uncertainties about the code for FPGA itself. The manual says to run provided batch files to upload specific .sof file to the FPGA, before running any C code for the PCIE. But there are only few example sets, so for a custom C code I will need to write custom .sof file to the FPGA as well. I did not find any guidelines or software examples about adapting the vhdl code to PCIE application. Can you provide any information (examples or pages, possibly documentation) about it? Thank you in advance.