Hello,
You can usually check your previous update.tar.gz to see what files are going to be overwritten. eg:
cd /usr/local/directadmin
tar tvzf update.tar.gz
which will dump out everything in it. It's pretty much guranteed that all of those files there will be overwritten with the new update.tar.gz. With things like skin updates, you may on occasion have new files for new features, etc..
Paste that, keep an eye on the versions system for what changes in the next udpate. We rarely touch any other system files, but we sometimes have to make "surgical" changes to others. For example, we needed to add 1 line to the exim.conf, so it's added with a perl regex, so your changes are not hurt.
For a list of things that are done in the update (outside of the DA files) you can look at the update.sh in the scripts directory. It's not updated often (many fixes are just rerun for each release, whch might not change anything if already implemented), but the update.sh is the only other thing done past the extraction of the update.tar.gz.
John