If you move it out of one server account it will be deleted when you're moving it. Remember there is a trash-folder in your account on the server where anything you delete (or move outside your account) will end up.

I have gone into Advanced account settings and selected to have new mail sent to my main mail account inbox. Now I have only one inbox and only one trash folder for all accounts. Not exactly what I wanted because now I don't have immediate visibility of which email id is receiving the mail.

It might work if you don't leave mails on the server. In IMAP are the mails from the other accounts showing up at that accounts inbox on the server (webmail) If so you could as well redirect it on server level and not download and then upload. What happen if you want to un-delete a message?

A solution would be send it to a local folder. That way it will be deleted on the mail server and you still have the opportunity to move it into one of the inboxes