I have been using eMclient probably 5 years. I was having a problem "send"ing emails. My husband tried to fix the problem…he wanted to change from POP to IMAP…he made an IMAP account…when he went back to transfer the files to POP account was gone…loosing all emails & Contacts. 
is there anyway to recover this…or is it gone???
Unfortunately when you delete the POP3 account, all the messages will be deleted, therefore the warning.
However, deleting the POP3 account would not have deleted the contacts so maybe that is not what happened. It would be best if your husband commented here as to what he did. Otherwise the only option is to restore from your most recent eM Client backup.
He had not deleted the POP account. and since I wrote this we have found contacts :) He never got the above “delete account” message.
So the POP3 account is still there in eM Client? (Deleting it and then adding it again will NOT restore the messages)
Without having deleted the account it is unlikely that the messages would have disappeared, unless you upgraded to a major version and did not accept the import option. So all I can suggest is to restore from your last backup then add the IMAP account, move the messages from the POP3 folder tree to the IMAP folder tree, and then delete the POP3 account.