The CLS compliance warnings can be safely ignored, and will be fixed in the next maintenance release.
The release notes on the Support menu will give detailed upgrading instructions. Typically, if just updating from one release to the next, the only thing you need to do is regenerate from the Generated Master template.
The Custom Master template just generates an empty partial class where you can add your custom code. You would usually not want to regenerate these, and wipe out all your hard work.
In fact, if you generate them into the same folder, the template has code in it that will prevent it from accidentally over-writing existing Custom classes.
You would definitely want to remove and re-add references if you are converting from the Trial to the purchased version. But, once you reference assemblies in the redistributables folder, any upgrade should over-write the old assemblies, and not require removing or re-adding references. Again, the release notes will contain specific instructions. For example, we changed the folder structure for the Ce assemblies after the 2007.0.0328 release.
David Neal Parsons
www.entityspaces.net