I was in a similar situation recently; actually I needed to re-use a cert from an earlier trial NE with a new version of the trial NE. I had partial success using
/opt/zimbra/bin/zmcertmgr deploycrt comm
(Must be run as root.)
See
zmcertmgr and
Administration Console and CLI Certificate Tools - Zimbra :: Wiki
Where I ran into trouble was with the intermediate and root certs, I believe. The commercial certificate is installed but the cert chain isn't complete as far as a web browser or other client is concerned. I would go back and try again but I've been busy with more pressing matters.
As for exporting a cert from Windows, I know that I've done it in the past. Here's a link that I turned up via a web search:
How to export a SSL certificate from Windows 2000 / 2003 server?
However, when I did it in the past, I was importing the cert into another IIS machine. I don't know if the format produced by Windows will be compatible with Zimbra, or if not, whether it can be massaged into the right format.