When upgrading from a older version of BAT you dont need to replace all the files, normaly replace the .dll/.so should be suffient. Its normaly smart to check the changelog to see if any new cvars have been added.
1) Shutdown the server ( You can use meta unload , but its a unsafe use at your own risk)
2) Upload the translation.dat file to addons/bat folder ( Changes to this file will rarely show up in the changelog , its recommended you update it regularly esp if your not using English as your default language).
3) Upload the new .dll / .so to the addons/bat/bin.
4) Check the changelog to see if any new cvars or other changes you need to check for. If there are any new cvars you can add them to your existing BATConfig.cfg file without any problems.
5) Restart your server ( or use meta load , if you use meta load change map right afterwards)