Gigabyte H310M conflicts with external hard drives

I’ve been having this issue on a computer on the hall for a few weeks now, its my boss’ PC and he’s getting impatient.
His computer has a Gigabyte H310M mb, and he uses an external HDD almost every day to back up his files, every once in a blue moon he forgets said HDD connected to that computer (almost every day actually) and sometimes that HDD conflicts with the machine’s internal drive, which leads to a boot failure.
When that happens, the boot drive on the computer simply vanishes from the BIOS and no matter how many times i restart it, it won’t show up again until i manually remove and reconnect it again.
I tried to disable some options in the BIOS like USB boot and fast boot, but the problem still persists.
We’ve also tried some hardware changes, we’ve changed the boot drive SSD’s brand (from an Adata SU-630 to a Maxtor Z1), sata cables, power supply and most importantly we’ve changed the external HDD setup, from an old WD 1tb drive to a brand new Toshiba 1tb disk with an Akasa case, that i’ve assembled myself, and the problem still persists.
I managed to replicate the issue various times with that set of hardware and with an additional external hard drive of my own (2TB Toshiba 3.5" disk on a wall powered Vantec case), i’ve also tried to replicate said issue on my computer, but being a vastly different machine, it didn’t happen.
It also has no pattern, it could take as much as 20 power cicles to appear, or as little as just 3.
I’ve also tried to RMA the motherboard, but the store wasn’t able to replicate this issue and it was ultimately returned.
Any idea as to what could be causing this, perhaps something i missed checking?

Is it directly connected to the back ports or to a front panel connector? Self powered drives need to be plugged into the back.

You might need to re-flash the BIOS because I feel it could be BIOS bit rot. The other thing is a ground loop somewhere.

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At the back, yes, on one of the USB 3.0 ports.

Sounds very plausible, just reflashing it with a current version should be enough? It came updated from the supplier to support the 9th gen CPU, so i haven’t tried to update it myself.

Yes, try to flash the BIOS again cause that could be what’s happening. That or the RAM is bad during boot.

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Turns out there’s 2 updates to the BIOS for it after the one currently installed, i’ll install those and see if there’s any positive effect.

@FurryJackman Updated it from F11 to F13, it took a while for it to accept the update, i even had to change the thumb drive.
For some reason it did not take version F12 at all, claiming there was an “OEM missmatch” or something along those lines.
It seems to be working alright so far.

Hmm, could be that the motherboard is confused that it’s an OEM motherboard rather than a retail one. You might need to fully clear the NVRAM.

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