Well thanks Apple. Awoke my iMac this morning to discover that El Capitan had been automatically upgraded in my absence to 10.11.1 which is supposed to have corrected the email set up bug. It has successfully recreated all the POP3 email accounts I had prior to original upgrade, but has lost all the On My Mac folders I had carefully recreated after the original upgrade mess. Also as El Capitan did not allow set up of POP3 accounts I had to set up all the accounts again using IMAP, which was a pain but didn't take too long. However, this latest upgrade has now left me with two versions of each Inbox, one POP3 and the other IMAP and one mailbox appears to have lost all of it's email, from both versions (admittedly, many of the messages in this box had been moved their by rules set up within Mail so may be retreivable).
So I now have to set up all the local folders again and check all the rules are there and working. Another wasted morning!!
El Capitan is the worst upgrade to a new version I have seen thus far.