diff --git a/init.sh b/init.sh
index 8851bba..8910fe4 100755
--- a/init.sh
+++ b/init.sh
@@ -465,20 +465,13 @@ initCheckConfigs() {
     # Check if any config files exist (new structure) or old config files
     local config_found=false
     
-    # Check for new structure
+    # Check for new structure. Skip subdirectories (per-location nested backup
+    # configs are loaded by their own helper) and the .category markers.
     if [ -d "$configs_dir" ]; then
         for category_dir in "$configs_dir"/*; do
             if [ -d "$category_dir" ] && [ -f "$category_dir/.category" ]; then
-                # Load new structure config files
                 for config_file in "$category_dir"/*; do
-                    local should_load=true
-                    local filename=$(basename "$config_file")
-                    # Skip .category files and excluded files (hardcoded)
-                    if [[ "$config_file" =~ \.category$ ]]; then
-                        should_load=false
-                    fi
-                    
-                    if [ "$should_load" = true ]; then
+                    if [ -f "$config_file" ] && [[ ! "$config_file" =~ \.category$ ]]; then
                         source "$config_file"
                         config_found=true
                     fi
@@ -1225,18 +1218,15 @@ reset_git_config() {
 
 # Helper function to load config files in the libreportal command
 commandReloadConfigs() {
-	# Load new structure config files only
+	# Load new structure config files only. Skip subdirectories (e.g. the
+	# per-location nested backup configs/backup/locations/<idx>/) — those are
+	# loaded by their own sourceBackupLocations helper. Skip the .category
+	# marker files too. Matches the guard initReloadConfigs / commandUpdateConfigOption
+	# already use.
 	for category_dir in "$configs_dir"/*; do
 		if [ -d "$category_dir" ] && [ -f "$category_dir/.category" ]; then
 			for config_file in "$category_dir"/*; do
-				local should_load=true
-				local filename=$(basename "$config_file")
-				# Skip .category files and excluded files (hardcoded for now)
-				if [[ "$config_file" =~ \.category$ ]]; then
-					should_load=false
-				fi
-				
-				if [ "$should_load" = true ]; then
+				if [ -f "$config_file" ] && [[ ! "$config_file" =~ \.category$ ]]; then
 					source "$config_file"
 				fi
 			done