diff --git a/app/core/src/main/java/stirling/software/SPDF/controller/api/MergeController.java b/app/core/src/main/java/stirling/software/SPDF/controller/api/MergeController.java
index 569c58f5ee5..b1132ec94f3 100644
--- a/app/core/src/main/java/stirling/software/SPDF/controller/api/MergeController.java
+++ b/app/core/src/main/java/stirling/software/SPDF/controller/api/MergeController.java
@@ -72,19 +72,29 @@ public PDDocument mergeDocuments(List<PDDocument> documents) throws IOException
     // fileOrder is newline-delimited original filenames in the desired order.
     private static MultipartFile[] reorderFilesByProvidedOrder(
             MultipartFile[] files, String fileOrder) {
-        String[] desired = fileOrder.split("\n", -1);
+        // Split by various line endings and trim each entry
+        String[] desired =
+                stirling.software.common.util.RegexPatternUtils.getInstance()
+                        .getNewlineSplitPattern()
+                        .split(fileOrder);
+
         List<MultipartFile> remaining = new ArrayList<>(Arrays.asList(files));
         List<MultipartFile> ordered = new ArrayList<>(files.length);
 
         for (String name : desired) {
-            if (name == null || name.isEmpty()) continue;
+            name = name.trim();
+            if (name.isEmpty()) {
+                log.debug("Skipping empty entry");
+                continue;
+            }
             int idx = indexOfByOriginalFilename(remaining, name);
             if (idx >= 0) {
                 ordered.add(remaining.remove(idx));
+            } else {
+                log.debug("Filename from order list not found in uploaded files: {}", name);
             }
         }
 
-        // Append any files not explicitly listed, preserving their relative order
         ordered.addAll(remaining);
         return ordered.toArray(new MultipartFile[0]);
     }
@@ -252,8 +262,10 @@ public ResponseEntity<StreamingResponseBody> mergePdfs(
 
         // If front-end provided explicit visible order, honor it and override backend sorting
         if (fileOrder != null && !fileOrder.isBlank()) {
+            log.info("Reordering files based on fileOrder parameter");
             files = reorderFilesByProvidedOrder(files, fileOrder);
         } else {
+            log.info("Sorting files based on sortType: {}", request.getSortType());
             Arrays.sort(
                     files,
                     getSortComparator(
diff --git a/app/core/src/main/resources/static/js/downloader.js b/app/core/src/main/resources/static/js/downloader.js
index 9e074be5e1c..070fd90af11 100644
--- a/app/core/src/main/resources/static/js/downloader.js
+++ b/app/core/src/main/resources/static/js/downloader.js
@@ -74,6 +74,12 @@
         showGameBtn.style.display = 'none';
       }
 
+      // Log fileOrder for debugging
+      const fileOrderValue = formData.get('fileOrder');
+      if (fileOrderValue) {
+        console.log('FormData fileOrder:', fileOrderValue);
+      }
+
       // Remove empty file entries
       for (let [key, value] of formData.entries()) {
         if (value instanceof File && !value.name) {
diff --git a/app/core/src/main/resources/static/js/merge.js b/app/core/src/main/resources/static/js/merge.js
index 01d7d97d998..09a4fe2fc17 100644
--- a/app/core/src/main/resources/static/js/merge.js
+++ b/app/core/src/main/resources/static/js/merge.js
@@ -123,39 +123,38 @@ function attachMoveButtons() {
   }
 }
 
-document.getElementById("sortByNameBtn").addEventListener("click", function () {
+document.getElementById("sortByNameBtn").addEventListener("click", async function () {
   if (currentSort.field === "name" && !currentSort.descending) {
     currentSort.descending = true;
-    sortFiles((a, b) => b.name.localeCompare(a.name));
+    await sortFiles((a, b) => b.name.localeCompare(a.name));
   } else {
     currentSort.field = "name";
     currentSort.descending = false;
-    sortFiles((a, b) => a.name.localeCompare(b.name));
+    await sortFiles((a, b) => a.name.localeCompare(b.name));
   }
 });
 
-document.getElementById("sortByDateBtn").addEventListener("click", function () {
+document.getElementById("sortByDateBtn").addEventListener("click", async function () {
   if (currentSort.field === "lastModified" && !currentSort.descending) {
     currentSort.descending = true;
-    sortFiles((a, b) => b.lastModified - a.lastModified);
+    await sortFiles((a, b) => b.lastModified - a.lastModified);
   } else {
     currentSort.field = "lastModified";
     currentSort.descending = false;
-    sortFiles((a, b) => a.lastModified - b.lastModified);
+    await sortFiles((a, b) => a.lastModified - b.lastModified);
   }
 });
 
-function sortFiles(comparator) {
+async function sortFiles(comparator) {
   // Convert FileList to array and sort
   const sortedFilesArray = Array.from(document.getElementById("fileInput-input").files).sort(comparator);
 
-  // Refresh displayed list
-  displayFiles(sortedFilesArray);
+  // Refresh displayed list (wait for it to complete since it's async)
+  await displayFiles(sortedFilesArray);
 
-  // Update the files property
-  const dataTransfer = new DataTransfer();
-  sortedFilesArray.forEach((file) => dataTransfer.items.add(file));
-  document.getElementById("fileInput-input").files = dataTransfer.files;
+  // Update the file input and fileOrder based on the current display order
+  // This ensures consistency between display and file input
+  updateFiles();
 }
 
 function updateFiles() {
@@ -163,25 +162,36 @@ function updateFiles() {
   var liElements = document.querySelectorAll("#selectedFiles li");
   const files = document.getElementById("fileInput-input").files;
 
+  console.log("updateFiles: found", liElements.length, "LI elements and", files.length, "files");
+
   for (var i = 0; i < liElements.length; i++) {
     var fileNameFromList = liElements[i].querySelector(".filename").innerText;
-    var fileFromFiles;
+    var found = false;
     for (var j = 0; j < files.length; j++) {
       var file = files[j];
       if (file.name === fileNameFromList) {
         dataTransfer.items.add(file);
+        found = true;
         break;
       }
     }
+    if (!found) {
+      console.warn("updateFiles: Could not find file:", fileNameFromList);
+    }
   }
+  
   document.getElementById("fileInput-input").files = dataTransfer.files;
+  console.log("updateFiles: Updated file input with", dataTransfer.files.length, "files");
 
   // Also populate hidden fileOrder to preserve visible order
   const order = Array.from(liElements)
     .map((li) => li.querySelector(".filename").innerText)
     .join("\n");
   const orderInput = document.getElementById("fileOrder");
-  if (orderInput) orderInput.value = order;
+  if (orderInput) {
+    orderInput.value = order;
+    console.log("Updated fileOrder:", order);
+  }
 }
 
 document.querySelector("#resetFileInputBtn").addEventListener("click", ()=>{