This is where good source management tools can help. In theory CVS can help you if you've set up your own CVS tree for your customizations and changes to OpenACS 4.5 files. It can do various kinds of merging of tree branches. But CVS isn't great at this which is one reason why folks are talking about investigating alternative tools for the future.
I'm not a CVS expert but if you look at Ron Henderson's piece on using CVS for web development at http::arsdigita.com/asj, he does talk a bit about how to set this up. So far I'm just concerning myself with setting up our own tree for release and development branches, a much simpler task.
If you're using OpenACS 4/PG then an important question is when did you start using it? Some of the datamodel has changed drastically in the last four months in the PG version and upgrading the datamodel won't be at all easy. That's why we recommended folks not use our alpha2 version for critical production sites.
From the beta forward (still looks like I can release tomorrow) we'll provide upgrade scripts for datamodel changes.
The Oracle side of things has been much more stable.
