@TheBW
I have done a few of these upgrades myself. One of the big things you want to do is move away from fedora and use CentOS CentOS is a supported server platform for Scalix, Fedora is not. Rememer as I know you are aware, Fedora is Redhat's Test bed before they roll any changes to thier flagship product. CentOS is an exact "copy" of redhat enterprise linux with out the "redhat" name. Redhat allows this and thats why there is CentOS. Redhat does not support CentOS, you have to go to the CentOS website for support.
Back to your question. You should back everything up first. IN other words shutdown the data base and do a full system backup.
Now do you have the /var/opt/scalix on a seperate volume? If you do, and what I have done in the past is not mounted the /var/op/scalix volume and did my OS install as well as the scalix install. This way your mail store is not touched. My suggestion is if you have a spare machine, setup a test server with your current version of the os and a simple install of scalix as it is. No need to copy the mail store over, then upgrade it and see what happens. I don't think it will clobber the current install but you can't be too careful these days.
Also you have to be careful with postgres database versions. my last upgrade I had an issue where the postgres database was at the wrong version and postgres would not start after the upgrade. Make sure you know the version of postgres so you know if you need to delete the postgres database after the upgrade. If you do need to delete the database, it will get created when postgres restarts.
but most of all, remember to back up. and allow for at lest 16 hours of work. an OS upgrade is not to be taken lightly. Again, I would recomend CentOS so that you dont have to upgrade as often.
-- Sideband Samurai