That's a tough one. Every way to flash the 3in1 I can think of requires using the DS lite.
Maybe it would be possible to use one of the old PC-based flashers, though those are made for other carts so I have no idea if it would work.
No need to help anymore, just found a way to fix. I noticed, that contacts, which cause system to reset are located on the left of the cart (if you look at the console normally). So I turned console on, put 3in1 somewhat diagonally, that the right side of 3in1 in not well connected - console resets, but don't regonize cart! then in slot-1 menu putting right side completely to the slot don't cause console to reset and GBAexploader regonizes slot-2 without problem.
I had same problem once with my 3in1 after flashing garbage to the Nor. But no matter how I positioned the cart, the console would instantly white screen. I couldn't seem to find the sweet spot. In the end I fixed it by flashing the 'FlashMe - no autoboot' firmware to my DS Lite. Held 'select+start' on boot to completely bypass the slot-2 detection check. Once in Wood I could flash something to Nor to fix the 3in1.