Startup trouble, won't update and says "operating system not found"

So when I tried updating to the new thunderbolt update thingy (yes I know, VERY late but I kept forgetting to update it and I didnt have time) it didnt start up because it said "operating system not found" after 30 mins of looking around for tips to reboot they didnt work,
I troed rebooting and it worked, and I followed the instructions to "download Mac OS X Lion" again. But it wont redownload because this reason:
"You can't upgrade this version of Mac OS X because a newer version is installed."
I have tried everything and since I downloaded the thunderbolt REALLY late I dont think anyone else had had this problem.
Help me please?

Hi, pimmerik. 
Thank you for visiting Apple Support Communities. 
Sorry to hear that you are experiencing this issue.  I would go through the steps in the article I have included below as they may help resolve this error. 
Mac OS X: Gray screen appears during startup
http://support.apple.com/kb/TS2570
Regards,
Jason H. 

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