Forum OpenACS Development: Response to Rename OpenACS Administration to Site-Wide Admin?
Not to be flippant, but the answer to your question is "very carefully".
Here's what I've been doing lately. I check out a copy of openacs-4 from the repo with the -kk switch (don't expand tags), and also a copy of our own installation from our CVS repo with -kk. Then I use Beyond Compare (an incredible diff utility--I can't speak highly enough about it, too bad it's Windows only) to compare the two trees. BC lets me compare the differences and copy files that have changed between the two trees. This way I can see if the data models have changed (without an accompanying upgrade script) and make the changes in our schema if necessary. Then I commit changes to our CVS repo.
Yes, it's a pain. The more cvs-ish option of doing a 'cvs import' doesn't let me see directly what has changed, though it would be faster. It's been taking me about an hour a day to track CVS this past week.