diff --git a/src/main/java/com/poratu/idea/plugins/tomcat/conf/TomcatCommandLineState.java b/src/main/java/com/poratu/idea/plugins/tomcat/conf/TomcatCommandLineState.java
index fda6bd6..06d27e6 100644
--- a/src/main/java/com/poratu/idea/plugins/tomcat/conf/TomcatCommandLineState.java
+++ b/src/main/java/com/poratu/idea/plugins/tomcat/conf/TomcatCommandLineState.java
@@ -120,7 +120,7 @@ protected JavaParameters createJavaParameters() {
 
             //copy to project folder, and then user is able to update server.xml under the project.
             Path projectConfPath = Paths.get(project.getBasePath(), ".smarttomcat", module.getName(), "conf");
-            if (!projectConfPath.toFile().exists()) {
+            if (!projectConfPath.toFile().exists() || PluginUtils.isEmptyFolder(projectConfPath)) {
                 FileUtil.createDirectory(projectConfPath.toFile());
                 FileUtil.copyDir(tomcatInstallationPath.resolve("conf").toFile(), projectConfPath.toFile());
             }
diff --git a/src/main/java/com/poratu/idea/plugins/tomcat/utils/PluginUtils.java b/src/main/java/com/poratu/idea/plugins/tomcat/utils/PluginUtils.java
index 33d6363..2ace189 100644
--- a/src/main/java/com/poratu/idea/plugins/tomcat/utils/PluginUtils.java
+++ b/src/main/java/com/poratu/idea/plugins/tomcat/utils/PluginUtils.java
@@ -309,4 +309,22 @@ public static List<Module> getModules(Project project) {
 
         return ModuleUtilCore.findModuleForFile(virtualFile, project);
     }
+
+    /**
+     * Checks if the given folder is empty.
+     *
+     * @param path the path to the folder
+     * @return {@code true} if the folder exists and is empty, {@code false} otherwise
+     * @throws IOException if an I/O error occurs
+     */
+
+    public static boolean isEmptyFolder(Path path) throws IOException {
+        if (Files.isDirectory(path)) {
+            try (Stream<Path> entries = Files.list(path)) {
+                return !entries.findFirst().isPresent();
+            }
+        }
+        return false;
+    }
+
 }