Marcus,
I'm using Artlantis Studio 2... But I'll bet this functionality has been maintained in later versions (I hope).
1. Save your current ATL file to a unique name (I add the date to the end of the name)
2. Open AC and save a new ATL file of the project.
3. Open the =new= ATL file in Artlantis.
4. Find 'Use Reference File' in the menu structure. Click it.
5. Pick your older version of the ATL file, and transfer whatever properties you desire from the items listed.
6. Smile and have a beer.
I do this all the time... We use Artlantis very early in the Design Development stage of the project to present progress to clients.
Hope that helps! If you need more detail, it's covered fairly well in the help files.