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Quite simply i have never really understood how to sort out issues concerning storage, but here's the lowdown:
Until very recently I had just the one SATA II drive
Today I installed another SATA II drive, however when I first booted into the BIOS to check that all drives were listed my original drive, with all the boot files, was no longer listed
As far as I know it should be possible to have multiple drives in a system, however the BIOS seems to only recognize one at a time, any ideas?
I had something similar, but my memory's failing me when it comes to a solution! I think it may have had something to do with AHCI mode (which I had turned on for an SSD) and turning it off again solved it.
I'd be inclined to try "silly" things like swapping ports first though. Stuff like that makes me feel like I'm doing something useful even when it's just a waste of time. My tolerance for troubleshooting hassle has definitely declined over the years.
Or maybe it's just my brain declining. :-)
I had a funny like that, I think it was because the first drive had a modern partition layout (was the only drive in there when Windows 7 was installed) but then when I plugged in an old drive with a traditional partition layout Windows would no longer boot.
It was a fresh Windows install for me, so I just re-installed Windows with the second disk already in the machine and it all worked. Still don't understand what that was all about.