diff --git a/tileserver/repository/reconfiguration/merge-config.js b/tileserver/repository/reconfiguration/merge-config.js
index 3e866a04..9e12225e 100644
--- a/tileserver/repository/reconfiguration/merge-config.js
+++ b/tileserver/repository/reconfiguration/merge-config.js
@@ -2,15 +2,41 @@
 // loss of mbtiles' metadata when the server is reconfigured. If the server is already running, it will require a restart
 // to apply the changes.
 
+// To prevent startup stalling, it also removes from the configuration file any references to mbtiles that are not
+// present in the server's data directory.
+
 const fs = require('fs');
 
 const baseConfigPath = process.argv[2];
 const configPath = process.argv[3];
 
+const fileExists = (path) => {
+    try {
+        return fs.existsSync(path);
+    } catch (e) {
+        return false;
+    }
+};
+
 try {
     const baseConfig = JSON.parse(fs.readFileSync(baseConfigPath, 'utf8'));
     const config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
+
+    // Remove data entries for missing mbtiles files
+    if (config.data && Array.isArray(config.data)) {
+        config.data = config.data.filter(tile => {
+            if (tile.file && !fileExists(tile.file)) {
+                console.log(`Removing missing tile file: ${tile.file}`);
+                return false; // Exclude this tile entry
+            }
+            return true;
+        });
+    }
+
+    // Merge the data from config into the base config
     baseConfig.data = config.data;
+
+    // Write the updated configuration back to the config file
     fs.writeFileSync(configPath, JSON.stringify(baseConfig, null, 2));
     console.log('Config merged successfully');
 } catch (error) {