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[SOLVED] Cloned my drive and now it won't boot back into my normal install!?

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Jul 16, 2012
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Motherboard
Lenovo Yoga 520 (Clover)
CPU
i7 7500U
Graphics
Intel 620, 1920x1080
Mac
  1. MacBook Pro
Mobile Phone
  1. iOS
I used Carbon Copy Cloner to clone my 1TB secondary drive to a new 3TB drive. After I did it, I swapped drives and now it doesn't boot properly. I use an SSD as my main drive and the HDD as a storage drive with all the main file directories linked on there (Music, Pictures, Movies, etc.).

See here:
http://imgur.com/J3yrmYZ
(Default El Capitan)

I swapped back the original 1TB drive in and the same issue occurs. I tried re-installing the boot loader with Multibeast on the main drive but still no luck. This is the first time i actually have no idea how to troubleshoot the problem and I can't find anyone who has or is having the same issue. Any possible solutions are welcome :)
 
Cloned my drive and now it won't boot back into my normal install!?

I used CCC to clone my secondary (storage) drive and after I cloned and swapped drives, my hackintosh booted into what seemed like a secondary install. Basically, it booted from my normal drive but into a default looking OSX, with no ability to open any of my apps or anything (hence why it seems like a completely different install, but i don't think it is). I then swapped the original drive back in and the same issue occurred.

Anyway, i think i know where to problem lies. It's got something to do with the recovery partition (or what ever that extra partition OSX adds onto a drive) because when i first loaded CCC, the drive was there, where as when the program failed and I had to re open it, it was gone. Maybe something went wrong in that stage but I don't really know. Basically, have you or anyone else have an idea of what might have happened? I'm currently trying to troubleshoot that possible issue now.

Edit: Spelling
 
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