I mean I know you have to copy the information into the file etc. 
   
  What I'm wondering is if it does replace the cert when you update to a
  new version. 
Nope, definitely not.  In general an upgrade should not
break/change anything. (That's the goal at least)
 
It will recreate certificates that don't exist, but I wouldn't expect
it to ever replace one that did exist.
  Also I put in a new cert but I sort of realized that it doesn't apply to
  the actual web server. Just the email SSL connections. Where is the web server
  based SSL for the back end located?  
The ssl is the same for both.  However, if you enabled per domain
certificates, then instead of 
    surgemail/ssl
you would need to copy the certificate(s) to
    surgemail/ssl/domain.name folders
 
So,  I'm not sure how this could have occurred.  Do let me know
if the situation repeats.
 
        ChrisP.
 
   
   
  ----- Original Message ----- 
   
  From: "Steven" <steve@wavedirect.org> 
  To: surgemail-list@netwinsite.com 
  Sent: Monday, September 9, 2013 10:44:53 AM 
  Subject: [SurgeMail List] SSL 
   
  When you upgrade an installation will it overwrite your SSL certificates?
  I just realized my cert isn't the official one I had anymore, its back to the
  self generated one. Nobody called in or anything about it either! If I recall
  all I had to do was copy the files into /usr/local/surgemail/ssl correct? I
  don't really need to do it in the web gui right?