Hello,
This sounds like a possible situation where Amazon cloud data isn't persisting in the way you expect, although I am by no means an EC2/AWS expert. An alternative explanation could be that it is plausible that you have some vulnerable application exposed (WordPress, Joomla!, and other CMS platforms sometimes have plugins that are quite vulnerable, for example), or even a phpMyAdmin instance with poor password security. If an attacker is able to gain access to your system, they could conceivably delete your data to be malicious. I probably couldn't guess which is a more likely.
I should assure you that phpMyAdmin has no means by which it automatically prunes data, and if you've got proper credentials with strong passwords for all of your accounts, it's rather unlikely that phpMyAdmin is at fault through negligence or flaw.
It's my understanding that an instance store-backed instance does not persist data after the instance is terminated (or fails), but again, it's not my area of expertise.
Good luck to you,
Isaac for the phpMyAdmin team