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I installed a second drive to my Mac Mini using iFixit's kit. Everything went fine except that now Finder doesn't see the original drive, even though it appears in the Disk Utility under its original name (Macintosh HD.)
I downloaded Yosemite and installed it on the new drive. (I opted for the 1TB Seagate with the SSD buffer.) The new drive seems to be working fine.
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First check your firmware level. Follow this Apple TN: EFI and SMC firmware updates for Intel-based Macs. Make sure you have the latest.
Sounds like you might have a bad SATA cable. Who's cable did you use and the PN#
Also did you swap the drives around by chance?
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That's because Finder doesn't normally show your main drive, even though that one isn't anymore, it was at one time. I don't know how to change it without wiping the drive with Disk Utility though.
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