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After 10.11.6 security and iTunes update, USB and SSD no longer bootable

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I was successfully running 10.11.6 and had previously updated from 10.11.5 successfully. Today I decided to install an update for iTunes. I had my Clover USB inserted, because I had been using that to boot into my OS X installation (Windows update had broken the default boot and I hadn't bothered to fix it quite yet).

Strangely, the update deleted everything on the USB EFI partition. I made another USB installer using Unibeast and didn't modify it at all. When booting to my Mac SSD, I get a freeze right at the Apple logo. Does anyone have any recommendations for the best path to recovery? I'm not exactly sure where to start. I tried searching the forums but only found one thread with my problem, and it had no replies.

Thanks in advance for any help!
 
I would like to know as well. I think I am in the same boat. Everything was fine for me after updating, but after a couple restarts I get stuck at the Apple logo and the progress bar never fills.

Thankfully I have windows 10 installed so I can load into that instead, but I need OSX for my music production software.
 
I had the same thing when I tried. I eventually had to reinstall OSX from USB key.

I later applied all updates one by one, EXCEPT the security one. I'm still waiting before doing that one.
 
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