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FacileManage on different port #20
Right now several bits of code rely on https running on port 443. So, yes, you would encounter issues if you changed it right now.
However, you could probably run your server on a non-443 port and update your client's config.inc.php to append :PORT to the FM_HOST variable. You'd have to do that manually as the client installer currently supports only 443. There is no manual workaround for your clients to run on a non-443 https port at this time though.
I've marked this issue to be fixed with 1.0-rc3.