How do I read and program the Up Squared V2 board using external EEPROM programmer?

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I have an Up Squared V2 board and I need to be able to read and program the UEFI/BIOS using an external EEPROM programmer. I have a CH341A programmer (https://instructables.com/CH341A-Programmer/) with a 1.8V adapter (the NOR Flash on the Up Squared V2 is a Winbond W25Q256JW 1.8 SPI NOR Flash). I am using the SNANDer and flashrom softwares on Linux and both fail during the probing process: both softwares read garbage as they try to identify which SPI NOR Flash is available. If I run the software multiple times, the garbage read during the probing process always change.

When I probed the SPI bus using a Saleae Logic Analyzer I could see the CH341A sending the commands but the output of the NOR Flash is random. I noticed that the voltage on the output pin is around 0.8V which is undefined!

The programming header on the Up Squared V2 board (CN1 connector) only contains six pins: VCC, GND, MOSI, MISO, CLK, and CS. I also noticed that the RESET/HOLD pin is not available.

Has anyone had this issue before? What did you do to fix this?

I also read on some forums and posts on the internet that people use the DediProg for this task. But these posts are about other versions of the Up Squared board family. I have not been able to find anything regarding Up Squared V2.

Flash Rom Error:

$ sudo ./flashrom -p ch341a_spi -r flash.bin -V
[sudo] password for (...): 
flashrom  on Linux 5.19.0-40-generic (x86_64)
flashrom is free software, get the source code at https://flashrom.org

Using clock_gettime for delay loops (clk_id: 1, resolution: 1ns).
flashrom was built with GCC 11.3.0, little endian
Command line (5 args): ./flashrom -p ch341a_spi -r flash.bin -V
Initializing ch341a_spi programmer
Device revision is 3.0.4 

This flash part has status NOT WORKING for operations: PROBE READ ERASE WRITE
This flash part has status UNTESTED for operations: WP
The test status of this chip may have been updated in the latest development
version of flashrom. If you are running the latest development version,
please email a report to [email protected] if any of the above operations
work correctly for you with this flash chip. Please include the flashrom log
file for all operations you tested (see the man page for details), and mention
which mainboard or programmer you tested in the subject line.
Thanks for your help!
Read is not working on this chip. Aborting

SNANder error:

$ ./SNANDer -r flash.bin

SNANDer - Serial Nor/nAND/Eeprom programmeR v.1.7.8b2 by McMCC <[email protected]>

Found programmer device: WinChipHead (WCH) - CH341A
Device revision is 3.0.4
spi_nand_probe: mfr_id = 0x2d, dev_id = 0xab, dev_id_2 = 0x92
SPI NAND Flash Not Detected!
spi device id: b0 ad f9 17 f0 (adf917f0)
SPI NOR Flash Not Detected!
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