diff --git a/scripts/upgrade b/scripts/upgrade
index ee82cfa..58dd47e 100755
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -51,7 +51,8 @@ ynh_app_setting_set --app="$app" --key=color --value="$color"
 ynh_script_progression --message="Upgrading source files..." --weight=3
 
 # Download, check integrity, uncompress and patch the source from app.src
-ynh_setup_source --dest_dir="$install_dir" --full_replace=1 --keep="config.php pheditor.php menu.php config.t2t var/pages/main.txt var/pages/todo.txt var/pages/sandbox.txt var/pages/links.txt var/pages/admin.txt"
+# ynh_setup_source --dest_dir="$install_dir" --full_replace=1 --keep="config.php pheditor.php menu.php config.t2t var/pages/main.txt var/pages/todo.txt var/pages/sandbox.txt var/pages/links.txt var/pages/admin.txt"
+ynh_setup_source --dest_dir="$install_dir" --keep="config.php pheditor.php menu.php config.t2t var/pages/main.txt var/pages/todo.txt var/pages/sandbox.txt var/pages/links.txt var/pages/admin.txt"
 
 
 chmod -R o-rwx "$install_dir"
@@ -73,8 +74,21 @@ ynh_backup_if_checksum_is_different --file="$install_dir/pheditor.php"
 ynh_delete_file_checksum --file="$install_dir/config.php"
 ynh_delete_file_checksum --file="$install_dir/pheditor.php"
 
-ynh_add_config --template="config.php" --destination="$install_dir/config.php"
-ynh_add_config --template="pheditor.php" --destination="$install_dir/pheditor.php"
+# Do not overwrite existing configuration as it could have user customization's and settings.
+# Create file if it does not exist
+if [ ! -f "$install_dir/config.php" ]; then
+	# Set the default settings
+	ynh_add_config --template="../conf/config.php" --destination="$install_dir/config.php"
+fi
+
+if [ ! -f "$install_dir/pheditor.php" ]; then
+	# Set the default settings
+	ynh_add_config --template="../conf/pheditor.php" --destination="$install_dir/pheditor.php"
+fi
+
+
+# ynh_add_config --template="config.php" --destination="$install_dir/config.php"
+# ynh_add_config --template="pheditor.php" --destination="$install_dir/pheditor.php"
 
 mkdir -p "$install_dir/templates/minimaxing/"
 ynh_delete_file_checksum --file="$install_dir/templates/minimaxing/minimaxing.less"