I sincerely hope you are not using the SVN repo, since it was abandoned. We use GIT. You can use the SVN client to pull from the GIT repo, so there's no problem, but if you used the SVN repo till this point, you will need to check yout a new server from the GIT repo. You can copy-paste your configs and npcs, so those and your stored data will be intact, but source mods will be gone.
If you used GIT previously, just do a regular update, and when prompted because of conflicts, choose as you wish (use server version/use your version/merge)