Hello,
DirectAdmin updates are generally safe and don't change anything. The file update.tar.gz is downloaded and extracted into the /usr/local/directadmin directory. It stores the binaries and any updates to skins (any skin changes to default or power_user would be overwritten). After the extraction, then /usr/local/directadmin/scripts/update.sh is run. This is generally empty and doesn't do anything of great importance. The exim.conf will not be overwritten, the main httpd.conf file will not be overwritten. If ever we need to make a change it would be done surgically meanining the line would be inserted and the whole file would not be overwritten.
John