so, just connecting CS on 11 instead of 5 ?
Yes, but posssibly keep 5 to GND also, i am not sure if the transistor is to drive CS low with the right timing.
It seems that it is possible on 12pin JSPI1, that pin 11 is WP and pin 12 is Hold, usually they should be connected to 3.3v.
If you got the multimeter maybe you can see what state pins 3&7 are.
EDIT: and CS to pin 9 not 11.
Hi Pacman!
I am now back home and was able to do testing with a proper multimeter.
So I am exactly in this situation for all pins except 9:
I have a transistor next to JSPI1 and bios, but it does not make contact between 5, 9 from JSPI1 to any of the transistor pin.
Maybe it’s not this one, but it’s the only one around.
So, i’m thinking of asking a friend (without parkinson’s disease) to old one multimeter pin on CS pin directly on bios, and link it to my raspberry while flashing. that should be doable.
And I will connect 11/12 to VCC.
//
I’m also attaching the image for future readers, in case someone needs and it’s not online anymore.
not working… either by keeping the CS directly on chip, or by connecting it to 5 and putting 9 to GND. I’m desperate now :’(
Ok, that was sad, if possible could you post a Picture of the setup, so the wiring to the PI is clearly shown?
Also, have you measured the 3.3v to the chip just to make sure?
EDIT: If the transistor is not connected to the JSPI1, then we can ignore that, but have you measure on all pins between the chip and JSPI1?
for example where does pin 5&9 go, if not to the transistor?
For now I removed my setup (it’s quite complicated to take as pic, because I have only independent wires, as the JSPI1 is not standard size header like front pannel or usb, it’s shorter spacement between pins).
I didn’t take live measurement (I’m always scared to do that)
I didn’t find where 5 and 9 pin go 
I found one topic somewhere earlier where the guys said he had to cut some connection from the chip to flash it because the motherboard totally protected it against flashing from outside, I wonder if I’m not in that case…
Ok, it may be he had to cut the Power Connection to the chip, it has been seen Before that sometimes it is needed.
But, in order to clear up the pinout situation first, if you can measure between the chip and JSPI1, while Everything of, to verify that the pinout on the image is correct.
For example pin 1 on the chip goes to ? pin on JSPI1, pin 2…
Oh sorry didn’t understand your question.
Yes I did that already, every pin is like the schema, except 9 and 5 which goes I don’t know where.
Apart from that, every JSPI1 pin goes where it should on the chip.
(and WP/HOLD goes to 11/12).
When I did my last tries, I connected 1/2/11/12 to VCC, 7/8 to GND (and I tried connecting also 9 after to GND), 3/4/6 to corresponding GPIO pin on RPI3, all of this from JSPI1 header.
And I asked a friend to manually hold a wire to CS0 on chip, which was going to corresponding GPIO header.
And flashrom didn’t find any chip :’(
Ok, that is very odd, do you have a soldering iron? as you have found, sometimes it is needed to sever the Connection between pin 8 on the chip and the motherboard, then apply Power to the chip directly.
Easiest way is just to use a soldering iron and lift pin 8.
Other than that, if you are 100% sure of the wiring to the PI, i am not sure what it might be, but also, how long are wires you are using, and what kind of wire is it?
Also, did you remove the battery on the motherboard?
wires are these:
https://www.amazon.fr/gp/product/B003HHR…0?ie=UTF8&psc=1
I removed the black plastic and kept only the wires.
it’s quite short
I wouldn’t like to use soldering iron because I will try to RMA the motherboard and I want it to be clean 
I did remove the battery yes
Yes, i am sorry i am not sure what may be the problem 
so at this Point it seems like RMA:ing the board is the best thing to do.
Anything else to try that i can Think of involves soldering.
I think this would have been a great thing to have but I don’t have time to wait delivery.
https://www.aliexpress.com/item/SOIC8-SO…c0-21931188b642
anyway, I agree with you. I would have love to flash it myself, but it seems I can’t.
Thanks a lot for all the help tho !
Yes, those clips are very good, i have a similar one, i hope Everything goes well with the RMA.
OK, I removed the motherboard from case (I didn’t until now) and found the transistor on other side. So I am exactly in the situation of the pic. But does that gives me any other solution ?
Well, just to be sure, you did measure and found that JSPI1 pin 5 & 9 goes to that transistor?
But, if you could test one thing?
If you wire it like this
First measure between JSPI1 5 & 7, 9 & 7 and see if there is any Connection there.
pin 17 on the pi to pin 1 JSPI1
pin 21 on the pi to pin 3 JSPI1
pin 19 on the pi to pin 4 JSPI1
pin 23 on the pi to pin 6 JSPI1
pin 25 on the pi to pin 7 JSPI1
pin 24 on the pi to pin 5 JSPI1 nothing to 9, then if nothing, with pin 9 to ground.
otherwise, then try pin 24 on the pi to pin 9 JSPI1 and nothing to pin 5, then ground to pin 5
Leave JSPI 11 & 12 unconnected at this time, if none of this works try only pin 12 to 3.3v.
I did lot of tries today, including testing my raspberry with some testspi.c I found online (confirmed it’s working), as well as changing to SPI1 instead of SPI0 (rpi3 have 2 SPIs on gpio port) => all same result.
When JSPI1 is connnected to PI, pi SPI reads only FFFFFF…, if disconnected, only 00000.
Tomorrow I don’t have much time, I’ll leave for maybe 2 weeks and send to RMA meanwhile… but if I can in morning, I’ll try these:
because previous one I tried already.
edit:
but why 11 or 12 unconnected ? i did testing with multimeter, they are linked directly to pin 3 and 7, which should be connected to VCC, isn’t it ?
edit2: MSI doesn’t want to RMA it, they want it to go through reseller, and reseller said it’s 2 years warranty, so I order a test clip, a new blank chip, and I’ll be back in 2 weeks (hopefully I don’t have soldering to do as I’m really bad at it…)
I just wanted to say: thank you very much! Just read out a Yoga 2 13 Bios chip, left out the cap (I’ll read it twice and check with md5sum). The Pi really is a swiss knife This is so cool!