diff --git a/scripts/upgrade b/scripts/upgrade
index f6fa371..b3b193d 100755
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -53,8 +53,13 @@ ynh_systemctl --service="$app" --action="stop"
 #=================================================
 ynh_script_progression "Upgrading source files..."
 
+### ynh_setup_source can wipe the destination dir if called with --full_replace.
+### On upgrade, that is certainly what you want, to remove any old source file that
+### does not exist in the new version of the software.
+### You can list with --keep every file/directory to *not* wipe or overwrite,
+### useful for configuration files, data directories, or plugins.
 # Download, check integrity, uncompress and patch the source from manifest.toml
-ynh_setup_source --dest_dir="$install_dir"
+ynh_setup_source --dest_dir="$install_dir" --full_replace --keep=".env data"
 
 ### $install_dir will automatically be initialized with some decent
 ### permissions by default ... however, you may need to recursively reapply