Most apps and files on my MacBook disappeared in front of my eyes.

Today I witness something exceptional:
I was running CleanMyMac2 (it was uninstalling some apps) while doing some other basic tasks (using Safari, iTunes). The CPU was working pretty hard and fans ran at full speed. After a few minutes, CleanMyMac seemed to be stuck. I did press the 'stop uninstall' (or something equivalent). All of a sudden, all of my applications and files started disappearing in front of my eyes! Literally! I opened the applications folder and one after another the icons disappeared. There are a few exceptions: my desktop files are still there and Xcode (which I hardly every use)... The dashboard also still works, but all utility applications are gone. My dock is filled with question marks. iStat menus is still running though. The files and apps are not in the Trash. Also the hard drive seems to be filled like it was before.
My MacBook Pro setup:
15inch i7 mbp mid 2010
8gb ram
1tb hd and 128gb ssd working together as an Apple fusion drive (I updated this about a month ago)
I did update to mavericks yesterday and everything worked fine.
I suspect that the 1tb hard drive has failed. Clearly the operations system is on the ssd to ensure optimal performance so that would explain why the system still boots. However, there are a few things that do make me doubt:
1) When I duplicate some large folders on the desktop and keep an eye on iStat menus, I see that the first 4gb will be written to the ssd, after that it still writes the remaining data to the 1tb hard drive.
2) I did boot in internet recovery mode and performed disk scans. No errors or problems have been found.
I'm getting a bit desperate. Your advice on what to do next is very much appreciated.
Bart

I restored the macbook from a time machine backup. Everything seems to work fine. Disk scans don't show errors and the weird sounds during shutdown are gone...
I still don't really trust the hard drive, though.

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While intending to perform a clean install of Mountain Lion while continuing with old apps and files, is it a waste to restore a backup that was made while running Mountain Lion as an UPgrade from Lion?
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Hello John!
Thank you for your response which solved my problem. For other users who may stumble upon this, I'll clear up the confusion and share how I solved the problem with your help; When looking for answers to my computer problems, finding unresolved questions where person B offers a solution and person A never comes back and says "That worked, thank you.", it demonstrates a "k-thnx-bye" user mentality that leaves others with the same problem lost. Without further ado:
It is not clear what you did because the meaning of "clean install" is vague. You can erase a volume and install an OS which leaves none of its previous content intact,
This is what I did: I erased the volume leaving no previous content intact, while then installing OS X Mountain Lion.
or you can upgrade an existing OS (or reinstall the same one) which does not alter your user - installed files.
An upgrade to Mountain Lion from Lion is what I started with initially before erasing anything. This was undesirable. Since this can cause Macs to run slower (especially whereas I'm using a mid-2011 Mac Mini), my goal was to go from operating within an upgrade to Mountain Lion, to operating within an installation of Montain Lion that was not preceded by any other oprating system.
Hence a "clean install of Mountain Lion while continuing with old apps and files" is confusing.
Well put and understood. What I should have said was:
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That makes sense and is just as I later suspected.
If so, how can I re-do the last portion of the process so that I get all my home-folder files and apps back without the full bulk of old Lion files? Migration assistant I'm guessing?
Yes.
This is what I did and everything works perfectly. Thank you so much once again!
-Chris

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Hi all,
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Most apps and files on my MacBook disappeared in front of my eyes.

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