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

I am not sure which ID is unidentified exactly (just pasted the error message). I provide a picture down below of the quartus logs, I hope it can introduce any additional info.

Regarding my accident with arduino, I did not connect any power, USB or any cables to arduino at all. I just plugged the arduino to the FPGA, but there were absolutely no other cables plugged to the arduino, my initial asumption was that FPGA should supply sufficient voltage and current to arduino by itself, and I wanted just a quick check (it gives me some hope because arduino itself does not generate any voltages, it can not produce anything beyond of what it is given or fed by FPGA.) After the accident, I identified a fried voltage regulator chip on the arduino. But just like I mentioned before, there were no such signs on the FPGA, and my voltage testing verified it.

I may lack the programming setup knowledge, but I need some guidance on further steps, do I:

1) Keep tweaking the programmer settings and trying to flash the memory?

2) Order brand new flash chip, replace it and hope that it should work properly?

3) Order brand new FPGA chip together with flash chip and replace them both?

4) Any other option?

If you need some more details, please let me know. Thank you.

I will provide some pictures of arduino and FPGA. Thats the best way to explain how did I try to connect one to another. On the other hand. I used the arduino Uno headers on the FPGA just like one would use to connect standard arduino uno shield, except I used arduino itself.

At some point flash memory usage is inevitable in my application. I need to preserve the FPGA code after power off.

Now I am waiting for the replacement flash memory chip to arrive. I did my research on replacing only the FPGA chip. I only found those at Mouser and DigiKey but the minimum amount is 40 at a unit price of 650 USD, so buying new devboard turns out way cheaper. I tested some of the FPGA pins. Both 7 segment displays dont work(I desoldered those and measured the voltages on the intended inputs on the PCB, I saw some random voltages like 1V, 1.5V 1.6V etc.) Also none of the four indicator leds works. I get constant 1.4V drop across those no mater the programmed pin state. LED0 is damaged itself (shows 0.078V drop across it on diode test mode.) But I measured every single one of the 2x20 GPIO connector pins with a 1 second led blink program. Surprisingly, every single pin in those connectors works normally. I am now trying to test if the PCIe will work, but since its my first time with it, it might take me a while to do it. For now thats all the information I can provide. Thank you for your help once again.

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.

It has been a long time since the last post, but now I have updates.

All these months were spent on testing and code development with still working IOs. Finally, I committed and replaced the main FPGA chip (Cyclone V 5CGTFD9D5F27C7N) with a new one to bring back 100% of the original board functionality. Desoldering and cleaning the pads went perfectly fine, soldering the new chip was also successful (can't have unquestionable proof, but the solder balls on the outer perimeter of the FPGA look really good, just like the old ones did). However, now my problem is that is can not flash my FPGA at all. I tried many different combinations, including an on-board integrated USB blaster also tried a Chinese clone as an external USB blaster. I tried JTAG, active and passive serial programming modes for FPGA and EPCQ256 but not a single combination and setup for flashing worked for me. Trying the JTAG I always get ,,chain error. No device detected", using other methods, I just get a failed programming sequence, without specification of the error/problem. I am still confident that my BGA soldering went well, I have thoroughly checked all the test points and voltages with my multimeter. I am getting all the 1.1V 1.8V 3.3V 5V 12V voltages, there are no excess heat or any shorts on the board. So I am pretty sure my soldering could not cause the problem. I am out of ideas what could be wrong here. I add a picture of both chips (for the possibility to check not only part numbers, but also batch codes), but its extremely unlikely that the new chip is defective/has a problem. On the other hand, I dont know any other solutions. I appreciate any observations and help. Thank you in advance.