@Raex-D: Yep, it's my understanding that whatever was happening here was anomalous, because the recovery's USB export option + initrd updater combo has never actually been seen deleting anything *on unplug*, ever.
Newer initrd updater *will* happily delete "invalid" (read: downgrade) updates on *boot*, though. But on USB unplug, nope, that's the OTA checker's prerogative.
What has been seen is the flash storage or the filesystem getting screwy behind your back.
Hence my comment: if the software didn't log a delete, yet the file disappeared, Gremlins be at work
. (Or PEBCAK, or miscommunication).
It's also not entirely impossible that Amazon did end up updating the recovery menu to do just that, though, hence my other remark about not necessarily trusting the *main* software version.
No real way to get to the bottom of it with unreadable logs, though
.