Oh dear, possible problem. There were a number of .emlx files that were emails. I'd already moved to the trash and deleted. Is that what you mean by email that arn't attachments?
Yes. Moving email will certainly corrupt the mailbox index which could cause you to lose additional email. To fix that simply rebuild each mailbox that you moved mail from.
More importantly, if you have IMAP accounts or POP accounts where you leave messages on the server, those emails will be downloaded to your Mac again the next time you check for new mail.
The correct way to go handle possibly infected emails is to choose "Reveal In Finder" for each one. When the window opens, double-click on the file to open it in your email client. If you decide you don't need to keep the message, use the email application's delete function to get rid of it on both your Computer and the server (gmail is a special case in that the only way to permanently delete an email is by using webmail in your browser, so you will have to hunt for it there). If you decide the message is something you need to keep then make note of the file number so you can ignore it the next time you scan.