Since upgrading to OSX El Capitan, I noticed one of my POP accounts keeps going offline. That account is hosted on Godaddy and after some web trawling it seems that Godaddy hosted POP email accounts won’t play nicely with Apple Mail under El Capitan. This may be the case with other hosting providers as well.

Thankfully, the solution is simple. Go to Preferences in Apple Mail and under the ‘Advanced’ tab there’s an option labeled ‘Automatically detect and maintain account settings’. If you
uncheck that box, your account will start working again.

Here’s a screen shot example:

I hope that’s of some help!