Sorry to hear about this.  I've been there.  I haven't had that experience with the Cloud, but before the cloud, I got into the habit of finding the prefs file, and after I'd created all my templates, zip the prefs for easy restoration later.  I still do this, in case the cloud isn't available for some reason.

I used to get corrupted prefs in Ae often before CC.  Not as much now.  I still get corrupted prefs way too often in Pr, though, and use the same strategy.  I even keep an alias of the prefs' containing folder on my desktop so that I can restore my prefs quickly and get back to work.

On Apr 7, 2014, at 11:35 AM, Teddy Gage <teddygage@gmail.com> wrote:

Now this is partially my fault for running too high of an overclock, but I had two separate crashes the other day that completely corrupted my prefs files, taking with it all custom workspaces (argh!) and output module templates (double argh!). These were not reset when I re-synced my downloaded creative cloud prefs, it seems they were lost forever.

When I restarted AE after the crash it says it could not find the prefs files and renamed all of them to .old - when I went into the .old files in wordpad, despite proper file sizes, they were completely empty. 

This is more or less a warning - I wish I had made full backups of my prefs, as it takes at least 45 minutes to re-create all the various settings and script panels and output modules as I like them. I had foolishly relied on the cloud to back up everything, and this is clearly not the case. At least I didn't lose any work

-TG

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VFX & Motion Graphic Artist
teddygage dot com