I observed that programming the BIOS with the oldest version of the BIOS can help, as ASUS BIOS somehow checks if the ME is in the chipset, and if not it programs it into the chipset from the BIOS chip during the first run after the BIOS programming.

Only what I can suggest is how to do it for ASUS board's. Unfortunately I don't know a good universal method to do it. If it's once happened to be missing in the chipset it needs to be reprogrammed again. As far as I understand the topic, the ME software needs to be programmed physically into the chipset's non-volatile memory to be working. One thing you can try is to force a reset using intel FPT ,flash programming tool using the command FPTW64.exe -greset ,and install the Management engine drivers from the motherboard support site or from winraid Have any of the PCH chips been replaced ? It could be a problem with the ME disable strap, or HDA_*** audio chip voltage. I speculate the chipset might be partly defective in those case, is it something really possible ? I even read the bios chip again after the first boot and checked if the ME was present and it was, so the ME is really on the bios chip but the board refuse to use it. Then after flashing and doing a full clear cmos and so on I still have the ME missing (detected as 'N/A') with some functionnality (depending on the board) missing such as frequency reading/overclocking and so on. I successfully flashed the bios using an external programmer with the bios file directly downloaded from the manufacturer and verified the ME was present (in the file) with the 'ME Analyser' python script.

Hi, I have a few different motherboard from different vendor and generation (Z77, Z87 and X99) that are 'missing' the Intel ME.

Intel fpt flash programming tool