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For the setup we are using, rolling the existing community AMI into an EBS volume and booting off that is a lot of work. The application data (including user uploaded files) is stored on an EBS volume, mounted, but all the server configuration is on instance store.

What is the probability that my instance will be killed and that my instance store data will be lost?

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Over a long enough time line, 100%. As Amazon makes changes to their network their servers occasionally restart and will take your instances with them. This page has some great information about persisting data across restarts, specifically, the section called "Persistence Strategy 2: S3-backed Instances".

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This is a good article; however, this assumes that EBS itself does not have a failure rate, which seems like an unreasonable assumption. However, moving stuff onto EBS makes it much easier to save a snapshot to S3. It's food for thought; what a shame Amazon can't just guarantee it! –  chrism2671 Sep 15 '10 at 11:44
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