I don’t quite understand. If the file was on an external drive, and it was disconnected – that would certainly explain why the encrypted file is damaged. But not how the original file was deleted. If it was on the same disconnected drive (and AxCrypt via the UI does not support encrypting to a different drive), the original can’t even in theory become deleted by AxCrypt – the drive is no longer connected!
If you did re-connect the drive, and then manually deleted the orginal, that of course would explain it.
And, sorry, no – there’s no way we can extract 599Mb from 16Mb…. With try broken file you should be able to recover the first aprox 16Mb, but that’s only about 2.5%…
If you actually did manually delete the original, there may be a chance that a regular undelete utility can recover it from your drive, provided you’ve not used the drive much or at all since the deletion.