Secondary SSD (2.5 SATA/AHCI) not initializing internally but still works via USB?

May 17, 2018
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I recently bought an Acer Aspire E5 Laptop because it comes with a 256GB M.2 SSD plus an empty 2.5" SATA slot for my 500GB Crucial BX100 SSD which I already own. Installation was easy -- the second SSD was recognized right away with all files accessible (no reformatting necessary) and everything worked fine for the first few days.

However, while testing the limits of the graphics card my system froze for a few minutes and I had to do a hard shutdown by holding the power button. After a longer-than-usual startup, the second drive was no longer showing up in Windows Explorer or the BIOS. However, it did appear in device manager as "Unknown Device" and disk management as "Disk 0 - Not Initialized" (the primary drive being Disk 1) but could not be initialized as GPT or MBR due to not having enough capacity.

After lots of trial and error, I determined it was not a hardware problem because (1) the SSD works fine when connected via USB to SATA adapter, and (2) the SATA port was still able to recognize other SATA drives with no issues. Eventually I was able to get it working again by doing a full factory reset.

A few weeks later I was doing some more heavy graphics processing and the system froze again requiring another hard shutdown. To my dismay, this produced the exact the same issue as before. I know I can fix it by doing another factory reset, but I'd rather not go that route if I can avoid it.

I have tried reinstalling/updating all firmware/drivers including Intel RST/RAID but that does not solve the problem. I am confident the issue is related to a corrupt UEFI/BIOS/Bootdisk or conflicting registry entry that manages the relationship between that particular port and this particular SSD.

So basically, is there any way to remove all traces of this SSD from the system so it can be reinstalled and initialized as if it's the first time being connected WITHOUT doing a factory reset?

EDIT: I was able to get the drive to work briefly by formatting it from NTFS to exFAT and renaming it while connected via USB, then reconnecting it to the SATA port. However, after a few minutes the drive disappeared again and went right back to the same unrecognized status. It still works fine via USB, however. If anything I think this only confirms my original theory that it's a BIOS or registry conflict.